format-version: 1.2 date: 11:04:2019 14:18 saved-by: pporras auto-generated-by: OBO-Edit 2.3.1 subsetdef: Drugable "Drugable Genome Project" subsetdef: PSI-MI_slim "Subset of PSI-MI" subsetdef: PSI-MOD_slim "subset of protein modifications" synonymtypedef: DeltaMass-label "Label from MS DeltaMass" EXACT synonymtypedef: PSI-MI-alternate "Alternate label curated by PSI-MI" EXACT synonymtypedef: PSI-MI-short "Unique short label curated by PSI-MI" EXACT synonymtypedef: PSI-MOD-alternate "Alternate label curated by PSI-MOD" EXACT synonymtypedef: PSI-MOD-short "Unique short label curated by PSI-MOD" EXACT synonymtypedef: PSI-MS-label "Agreed label from MS community" RELATED synonymtypedef: RESID-alternate "Alternate name from RESID" EXACT synonymtypedef: RESID-misnomer "Misnomer label from RESID" RELATED synonymtypedef: RESID-name "Name from RESID" EXACT synonymtypedef: RESID-systematic "Systematic name from RESID" EXACT synonymtypedef: UniMod-alternate "Alternate name from UniMod" RELATED synonymtypedef: UniMod-description "Description (full_name) from UniMod" RELATED synonymtypedef: UniMod-interim "Interim label from UniMod" RELATED synonymtypedef: UniMod-label "Label (title) from UniMod" RELATED synonymtypedef: UniProt-feature "Protein feature description from UniProtKB" EXACT default-namespace: PSI-MI remark: Notes: remark: Each of the top level terms in this file is the root term of an independent controlled vocabulary remark: mapping an element of the PSI Molecular Interaction XML schema. remark: The correct use of these vocabularies in the PSI Molecular Interaction XML schema is remark: formalized in a mapping file available at http://www.psidev.info/files/validator/xml/MI-CVMapping.xml. remark: The PSI MI schema defines short labels for controlled vocabulary terms remark: short labels are reported as PSI-MI-short synonyms that are created when a term is more than 20 characteres long. remark: The last accession number used in this file is stored in a separate file, remark: psi-mi.lastac. It MUST be updated when this file is updated. remark: The maintenance of this file is ensured by Sandra Orchard orchard@ebi.ac.uk and Luisa Montecchi Palazzi luisa@ebi.ac.uk remark: coverage: This file collect controlled vocabularies describing different aspects of molecular interactions. remark: publisher: This file is published by the PSI MI working group see http://psidev.info/MI remark: CVversion: 2.5.5 ontology: mi [Term] id: MI:0000 name: molecular interaction def: "Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "mi" EXACT PSI-MI-short [] [Term] id: MI:0001 name: interaction detection method def: "Method to determine the interaction." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "interaction detect" EXACT PSI-MI-short [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0002 name: participant identification method def: "Method to determine the molecules involved in the interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "participant detection" EXACT PSI-MI-alternate [] synonym: "participant ident" EXACT PSI-MI-short [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0003 name: feature detection method def: "Method to determine the features of the proteins involved in the interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "feature detection" EXACT PSI-MI-short [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0004 name: affinity chromatography technology def: "This class of approaches is characterised by the use of affinity resins as tools to purify molecule of interest (baits) and their binding partners. The baits can be captured by a variety of high affinity ligands linked to a resin - for example, antibodies specific for the bait itself, antibodies for specific tags engineered to be expressed as part of the bait or other high affinity binders such as glutathione resins for GST fusion proteins, metal resins for histidine-tagged proteins." [PMID:7708014] subset: PSI-MI_slim synonym: "affinity chrom" EXACT PSI-MI-short [] synonym: "Affinity purification" EXACT PSI-MI-alternate [] is_a: MI:0091 ! chromatography technology is_a: MI:0400 ! affinity technology [Term] id: MI:0005 name: alanine scanning def: "This approach is used to identify the residues that are involved in an interaction. Several variants of the native protein are prepared by sequentially mutating each residue of interest to an alanine. The mutated proteins are expressed and probed in the binding assay." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0810 ! substitution analysis [Term] id: MI:0006 name: anti bait coimmunoprecipitation def: "A specific antibody for the molecule of interest (bait) is available, this is used to generate a high affinity resin to capture the endogenous bait present in a sample." [PMID:7708014] subset: PSI-MI_slim synonym: "anti bait coip" EXACT PSI-MI-short [] is_a: MI:0019 ! coimmunoprecipitation [Term] id: MI:0007 name: anti tag coimmunoprecipitation def: "A specific antibody for the molecule of interest is not available, therefore the bait protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient and specific antibodies or a specific ligand are available." [PMID:7708014] subset: PSI-MI_slim synonym: "anti tag coip" EXACT PSI-MI-short [] is_a: MI:0019 ! coimmunoprecipitation [Term] id: MI:0008 name: array technology def: "In this class of methodologies, the molecules to be tested are presented ordered in an array format (typically at high density) on planar supports. The characteristics and chemical nature of the planar support can vary. This format permits the simultaneous assay, in controlled conditions, of several thousand proteins/peptides/nucleic acids for different functions, for instance their ability to bind any given molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0400 ! affinity technology [Term] id: MI:0009 name: bacterial display def: "The protein of interest is presented on the outer membrane of Gram negative bacteria by expressing it as a fusion partner to peptide signals that direct heterologous proteins to the cell surface. For instance, a single chain Fv (scFv) antibody fragment, consisting of the variable heavy and variable light domains from two separate anti-digoxin monoclonal antibodies, was displayed on the outer membrane of Escherichia coli by fusing it to an Lpp-OmpA. Similar systems have also been developed for gram positive bacteria. Fluorescence-activated cell sorting (FACS), is used to specifically select clones displaying a protein binding to scFv-producing cells." [PMID:10436088, PMID:8248129] subset: PSI-MI_slim is_a: MI:0034 ! display technology is_a: MI:0054 ! fluorescence-activated cell sorting [Term] id: MI:0010 name: beta galactosidase complementation def: "Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the success of this system is the choice of two poorly complementing mutant moieties, since strongly complementing mutants spontaneously assemble and produce functional beta-gal activity detectable in absence of any fused protein fragment." [PMID:12042868, PMID:9237989] subset: PSI-MI_slim synonym: "beta galactosidase" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0011 name: beta lactamase complementation def: "This strategy is based on a protein fragment complementation assay (PCA) of the enzyme TEM-1 beta-lactamase. The approach includes a simple colorimetric in vitro assays using the cephalosporin nitrocefin and assays in intact cells using the fluorescent substrate CCF2/AM. The combination of in vitro colorimetric and in vivo fluorescence assays of beta-lactamase in mammalian cells permits a variety of sensitive and high-throughput large-scale applications." [PMID:12042868] subset: PSI-MI_slim synonym: "beta lactamase" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0012 name: bioluminescence resonance energy transfer def: "In this variation of the FRET assay the donor fluorophore is replaced by a luciferase (typically Renilla luciferase). In the presence of its substrate, the luciferase catalyses a bioluminescent reaction that excites the acceptor fluorophore through a resonance energy transfer mechanism. As with FRET the energy transfer occurs only if the protein fused to the luciferase and the one fused to the acceptor fluorophore are in close proximity (10-100 Angstrom)." [PMID:9874787, PMID for application instance:10725388] subset: PSI-MI_slim synonym: "BRET" EXACT PSI-MI-alternate [] synonym: "bret" EXACT PSI-MI-short [] synonym: "LRET" EXACT PSI-MI-alternate [] is_a: MI:0051 ! fluorescence technology [Term] id: MI:0013 name: biophysical def: "The application of physical principles and methods to biological experiments." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0045 ! experimental interaction detection [Term] id: MI:0014 name: adenylate cyclase complementation def: "Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary complex. In the absence of calmodulin, the mixture of the two fragments does not exhibit detectable activity, suggesting that the two fragments do not associate. When expressed in an adenylate cyclase-deficient E. coli strain (E. coli lacks calmodulin or calmodulin-related proteins), the T25 and T18 fragments fused to putative interacting proteins are brought into close association which result in cAMP synthesis. The level of reconstructed adenylate cyclase can be estimated by monitoring the expression of a cAMP dependent reporter gene. The T25 tagged protein is generally regarded as the bait, the T18 as the prey." [PMID:9576956] subset: PSI-MI_slim synonym: "adenylate cyclase" EXACT PSI-MI-short [] synonym: "bacterial two-hybrid" EXACT PSI-MI-alternate [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0016 name: circular dichroism def: "Circular dichroism (CD) is observed when optically active molecules absorb left and right hand circularly polarized light slightly differently. Linearly polarized light can be viewed as a superposition of two components of circularly polarized light of equal amplitude and phase but opposite handness. When this light passes through an optically active sample the two polarized components are absorbed differently. The difference in left and right handed absorbance A(l)- A(r) is the signal registered in CD spectra. This signal displays distinct features corresponding to different secondary structures present in peptides, proteins and nucleic acids. The analysis of CD spectra can therefore yield valuable information about the secondary structure of biological macromolecules and the interactions among molecules that influence their structure." [PMID:11578931] subset: PSI-MI_slim synonym: "CD" EXACT PSI-MI-alternate [] synonym: "cd" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical [Term] id: MI:0017 name: classical fluorescence spectroscopy def: "Proteins contain endogenous fluorophores such as tryptophan residue and heme or flavins groups. Protein folding and protein-protein interaction can be studied by monitoring changes in the tryptophan environment detected by changes in its intrinsic fluorescence. Changes in the fluorescence emission spectrum on complex formation can occur either due to a shift in the wavelength of maximum fluorescence emission or by a shift in fluorescence intensity caused by the mixing of two proteins. The interaction of two proteins causes a shift in the fluorescence emission spectrum relative to the sum of the individual fluorescence spectra, resulting in a difference spectrum [F (complex)-2 F (sum)], which is a measurable effect of the interaction. Loss of fluorescence signal from a substrate can be used to measure protein cleavage." [PMID:7708014] subset: PSI-MI_slim synonym: "fluorescence spectr" EXACT PSI-MI-short [] is_a: MI:0051 ! fluorescence technology [Term] id: MI:0018 name: two hybrid def: "The classical two-hybrid system is a method that uses transcriptional activity as a measure of protein-protein interaction. It relies on the modular nature of many site-specific transcriptional activators (GAL 4) , which consist of a DNA-binding domain and a transcriptional activation domain. The DNA-binding domain serves to target the activator to the specific genes that will be expressed, and the activation domain contacts other proteins of the transcriptional machinery to enable transcription to occur. The two-hybrid system is based on the observation that the two domains of the activator need to be non-covalently brought together by the interaction of any two proteins. The application of this system requires the expression of two hybrid. Generally this assay is performed in yeast cell, but it can also be carried out in other organism. The bait protein is fused to the DNA binding molecule, the prey to the transcriptional activator." [PMID:10967325, PMID:12634794, PMID:1946372] subset: PSI-MI_slim synonym: "2 hybrid" EXACT PSI-MI-short [] synonym: "2-hybrid" EXACT PSI-MI-alternate [] synonym: "2H" EXACT PSI-MI-alternate [] synonym: "2h" EXACT PSI-MI-alternate [] synonym: "classical two hybrid" EXACT PSI-MI-alternate [] synonym: "Gal4 transcription regeneration" EXACT PSI-MI-alternate [] synonym: "two-hybrid" EXACT PSI-MI-alternate [] synonym: "Y-2H" RELATED [] synonym: "Y2H" EXACT [] synonym: "yeast two hybrid" EXACT PSI-MI-alternate [] is_a: MI:0232 ! transcriptional complementation assay [Term] id: MI:0019 name: coimmunoprecipitation def: "In this approach an antibody, specific for the molecule of interest (bait) or any tag expressed within a fusion protein, is used to separate the bait from a molecular mixture or a cell lysate and to capture its ligand simultaneously. The partners that bind to the bait molecule retained by the resin can then be eluted and identified. The antibody may be free or bound to a matrix during this process." [PMID:7708014] subset: PSI-MI_slim synonym: "co-immunoprecipitation" EXACT PSI-MI-alternate [] synonym: "Co-IP" EXACT PSI-MI-alternate [] synonym: "CoIp" EXACT PSI-MI-alternate [] synonym: "coip" EXACT PSI-MI-short [] synonym: "immunoprecipitation" EXACT PSI-MI-alternate [] is_a: MI:0004 ! affinity chromatography technology [Term] id: MI:0020 name: transmission electron microscopy def: "During the treatment for microscope analysis a tissue section is incubated with high-specificity antibodies coupled to heavy metals (gold). Any tissue section can then be analysed by electron microscopy to localise the target proteins within the cell. This method supports very high resolution colocalisation of different molecules in a cell." [PMID:14755292] subset: PSI-MI_slim synonym: "tem" EXACT PSI-MI-short [] is_a: MI:0040 ! electron microscopy [Term] id: MI:0021 name: colocalization by fluorescent probes cloning def: "Two proteins can be localised to cell compartments, in the same experiment, if they are expressed as chimeric proteins fused to distinct proteins fluorescing at different wavelengths (Green Fluorescent Protein and Red Fluorescent Protein for example). Using a confocal microscope the two proteins can be visualized in living cells and it can be determined whether they have the same subcellular location. Fluorescence microscopy of cells expressing a GFP fusion protein can also demonstrate dynamic processes such as its translocation from one subcellular compartment to another.\nOBSOLETE: use imaging technique (MI:0428) and specific probe as feature of each interacting protein." [PMID:14755292] subset: PSI-MI_slim synonym: "coloc fluoresc probe" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0022 name: colocalization by immunostaining def: "The subcellular location of a protein can be demonstrated by treating cells fixed on a microscope slide with an antibody specific for the protein of interest. A secondary antibody conjugated with a reactive enzyme (e.g. horseradish peroxidase) is then added. Following a washing step to remove the unbound secondary ligand, a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme and can then be visualised by standard microscopic techniques.\nOBSOLETE since combination of Interaction Detection Method and Interaction Type.Consider using the Interaction Detection Method imaging techniques (MI:0428) coupled with Interaction Type colocalisation (MI:0403) and Participant detection immunostaining (MI:0422) instead." [PMID:14755292] subset: PSI-MI_slim synonym: "coloc immunostaining" EXACT PSI-MI-short [] synonym: "Immunofluorescence Staining" EXACT PSI-MI-alternate [] synonym: "Immunostaining" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0023 name: colocalization/visualisation technologies def: "Techniques enabling the identification of the subcellular localisation of a protein or complex. Two different proteins show a similar distribution in the cell are said to co-localise. Obsolete since combination of Interaction Detection Method and Interaction Type.\nOBSOLETE. Consider using imaging techniques (MI:0428) as interaction detection method coupled with colocalisation (MI:0401) as interaction type and predetermined (MI:0396) as participant detection." [PMID:14755292] subset: PSI-MI_slim synonym: "coloc visual technol" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0024 name: confirmational text mining def: "Text mining is used to support interactions which have been determined by other methods." [PMID:14755292] subset: PSI-MI_slim synonym: "conformational tm" EXACT PSI-MI-short [] is_a: MI:0110 ! text mining [Term] id: MI:0025 name: copurification def: "Approaches designed to separate cell components on the basis of their physicochemical properties. The observation that two or more proteins copurify in one or several conditions is taken as an indication that they form a molecular complex.\nOBSOLETE since too non-specific. Consider use of cosedimentation (MI:0027) or comigration in non denaturing gel electrophoresis (MI:0404) or affinity chromatography technologies (MI:0004) or molecular sieving (MI:0071) or for unspecific cases biochemical (MI:0401)." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0026 name: correlated mutations def: "Pairs of multiple alignments of orthologous sequences are used to identify potential interacting partners as proteins that show covariation of their residue identities between different species. Proteins displaying inter-protein correlated mutations during evolution are likely to be interacting proteins due to co-adapted evolution of their protein interacting interfaces." [PMID:11933068] subset: PSI-MI_slim is_a: MI:0101 ! sequence based prediction is_a: MI:0660 ! feature prediction [Term] id: MI:0027 name: cosedimentation def: "Separation of a mixture of molecules under the influence of a force such as artificial gravity. Molecules sedimenting together are assumed to interact." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0401 ! biochemical [Term] id: MI:0028 name: cosedimentation in solution def: "The ultracentrifuge can be used to characterise and/or purify macromolecules in solution according to their mass and hydrodynamic properties. Sedimentation studies provide information about the molecular weight and shape of a molecule. It is also possible to measure the association state of the sample. Both the mass of a molecule and its shape, that influences the friction forces and diffusion that counterbalances gravity, determine the sedimentation speed." [PMID:10410796] subset: PSI-MI_slim synonym: "solution sedimentati" EXACT PSI-MI-short [] is_a: MI:0027 ! cosedimentation [Term] id: MI:0029 name: cosedimentation through density gradient def: "Sedimentation through a density gradient measures the sedimentation rate of a mixture of proteins through either a glycerol or sucrose gradient. Two interacting proteins will sediment mostly as a complex at concentrations above the binding constant. By varying the concentration of one or both of the complex constituents and taking into account the dilution of the species during sedimentation, one can reasonably accurately estimate the binding constant." [PMID:10410796] subset: PSI-MI_slim synonym: "density sedimentation" EXACT PSI-MI-short [] is_a: MI:0027 ! cosedimentation [Term] id: MI:0030 name: cross-linking study def: "Analysis of complexes obtained by input of energy or chemical treatments, or by introducing cysteines followed by oxidation to promote the formation of covalent bonds among molecules in close proximity." [PMID:14755292] subset: PSI-MI_slim synonym: "crosslink" EXACT PSI-MI-short [] is_a: MI:0401 ! biochemical [Term] id: MI:0031 name: protein cross-linking with a bifunctional reagent def: "Cross-linking agents induce the formation of covalent bonds among proteins that are neighbours. The cross-linker may be a bifunctional molecule having two reactive ends linked by a spacer, often containing a disulfide bond. When a reducing agent is added the disulfide bridge is cleaved, the cross-linked pairs are released and can be identified. There are various classes of cross-linkers, the most common are those having photoreactive groups that become reactive fluorophores when activated by UV light thereby resulting in photolabeling the cross-linked moieties." [PMID:10679368, PMID:7708014] subset: PSI-MI_slim synonym: "bifunctional agent crosslink" EXACT PSI-MI-short [] synonym: "Label transfer techniques" EXACT PSI-MI-alternate [] synonym: "Photoaffinity labelling" EXACT PSI-MI-alternate [] is_a: MI:0030 ! cross-linking study [Term] id: MI:0032 name: de novo protein sequencing by mass spectrometry def: "The strategy to determine the complete amino acid sequence of a protein by mass spectrometry relies on the generation of a nested set of fragments differing by one amino acid. This reveals the identity of the residue that has been removed at each degradation step by measuring the mass difference of fragments differing of one residue. Peptide fragments can be obtained by protease treatment combined with the fragmentation promoted by collision (or other methods) within a tandem mass spectrometer. This approach can be carried out with LC MS/MS (Liquid Chromatography Tandem Mass Spectrometry), nanoESI MS/MS (nanoElectrospray Ionisation tandem mass spectrometry), or FTMS (Fourier Transform mass spectrometry) instruments." [PMID:10984529] subset: PSI-MI_slim synonym: "de novo protein sequence" EXACT PSI-MI-short [] synonym: "MS/MS" RELATED [] is_a: MI:0093 ! protein sequence identification is_a: MI:0427 ! Identification by mass spectrometry is_a: MI:0659 ! experimental feature detection [Term] id: MI:0033 name: deletion analysis def: "In this approach, once a molecule is demonstrated to participate in an interaction, several deletion derivatives are produced and tested in the binding assay to identify the minimal fragment (domain) that can still support the interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0074 ! mutation analysis [Term] id: MI:0034 name: display technology def: "All the methods that permit the physical linking of a protein/peptide to its coding sequence. As a consequence affinity purification of the displayed peptide results in the genetic enrichment of its coding sequence. By these technologies genes encoding a peptide with desired binding properties can be selected over an excess of up to 1012 unrelated molecules." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0400 ! affinity technology [Term] id: MI:0035 name: docking def: "Predicts the structure of a molecular complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid objects. Initial scoring of a complex is based on geometric fit or surface complementarity. This generally requires some knowledge of the binding site to limit the number of solutions." [PMID:9631301, PMID for application instance:11478868] subset: PSI-MI_slim is_a: MI:0105 ! structure based prediction is_a: MI:0577 ! feature prediction from structure [Term] id: MI:0036 name: domain fusion def: "The rosetta stone, or domain fusion procedure, is based on the assumption that proteins whose homologues in other organisms happen to be fused into a single protein chain are likely to interact or to be functionally related." [PMID:10573422] subset: PSI-MI_slim synonym: "Rosetta Stone" EXACT PSI-MI-alternate [] is_a: MI:0058 ! genome based prediction is_a: MI:0101 ! sequence based prediction [Term] id: MI:0037 name: domain profile pairs def: "This approach uses a protein interaction network of a given organism to infer interaction in another organism using information about the interacting region. The regions or domains involved in interactions are clustered if they share sequence similarity and have common interacting partners. The resulting domain profiles are then used to screen the proteome of another organism and domain-domain interactions are inferred. Ultimately, an inferred protein interaction map is built in this second organism." [PMID:11473021] subset: PSI-MI_slim is_a: MI:0046 ! experimental knowledge based is_a: MI:0101 ! sequence based prediction is_a: MI:0660 ! feature prediction [Term] id: MI:0038 name: dynamic light scattering def: "In dynamic light scattering, particle diffusion in solution gives rise to fluctuations in the intensity of the scattered light on the microsecond scale. The hydrodynamic radius of the particles can be easily calculated." [PMID:9013660] subset: PSI-MI_slim synonym: "dls" EXACT PSI-MI-short [] is_a: MI:0067 ! light scattering [Term] id: MI:0039 name: edman degradation def: "In this procedure the N-terminus amino acid is cleaved from a polypeptide and identified by high-pressure liquid chromatography. The cycle is repeated on the ever-shortening polypeptide until all the residues are identified. On average only 20-30 consecutive cycles can be performed and lead to amino acid identification. Longer polypeptides or full length proteins must be cleaved by specific protease before Edman degradation and their sequences built by fragment overlapping." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0433 ! partial identification of protein sequence [Term] id: MI:0040 name: electron microscopy def: "Electron microscopy methods provide insights into the structure of biological macromolecules and their supramolecular assemblies. Resolution is on average around 10 Angstroms but can reach the atomic level when the samples analysed are 2D crystals. Different types of samples can be analysed by electron microscopy: crystals, single particles like viruses, macromolecular complexes or entire cells and tissue sections. Samples can be chemically fixed or vitrified by rapid freezing in liquid ethane, and then transferred into the electron microscope. Data collection consists of the recording of electron diffraction data (2D crystals) and images. Depending on the type of sample, different approaches are used to analyse and merge images and electron diffraction data." [PMID:11785754] subset: PSI-MI_slim synonym: "Electron cryomicroscopy" EXACT PSI-MI-alternate [] synonym: "Electron crystallography" EXACT PSI-MI-alternate [] is_a: MI:0428 ! imaging technique [Term] id: MI:0041 name: electron nuclear double resonance def: "A combination of NMR and EPR. The lines in the EPR spectrum that are caused by coupling of an unpaired electron nearby nuclei change in intensity when these nuclei are excited at their NMR frequency." [PMID:11817959, PMID:11988476, PMID for application instance:12186859] subset: PSI-MI_slim synonym: "ENDOR" EXACT PSI-MI-alternate [] synonym: "endor" EXACT PSI-MI-short [] is_a: MI:0043 ! electron resonance [Term] id: MI:0042 name: electron paramagnetic resonance def: "EPR (also called ESR, Electron Spin Resonance) spectroscopy is analogous to NMR, but is based on the excitation of unpaired electrons instead of nuclei. Unpaired (single) electrons are only found in radicals and some metal ions (paramagnetic species); the EPR spectrum provides information about the environment and mobility of the paramagnetic species. The magnetic interaction of two paramagnetic centres in a protein can be used to calculate the distance between them; this allows studies of the movements and interactions of protein segments. In proteins without any intrinsic unpaired electrons it is possible to attach a radical probe (spin label). Stable nitroxide radicals can be bound to amino acid residues, in analogy with fluorescent probes. In combination with site directed mutagenesis this method is used in particular to study structure and assembly of membrane proteins, by measuring with EPR whether an amino acid is in a polar or non polar environment." [PMID:11817959] subset: PSI-MI_slim synonym: "EPR" EXACT PSI-MI-alternate [] synonym: "epr" EXACT PSI-MI-short [] synonym: "ESR" EXACT PSI-MI-alternate [] is_a: MI:0043 ! electron resonance [Term] id: MI:0043 name: electron resonance def: "A form of spectroscopy in which the absorption of microwave by a sample in a strong magnetic field is used to study atoms or molecules with unpaired electrons." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0013 ! biophysical is_a: MI:0659 ! experimental feature detection [Term] id: MI:0045 name: experimental interaction detection def: "Methods based on laboratory experiments to determine an interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "experimental interac" EXACT PSI-MI-short [] is_a: MI:0001 ! interaction detection method [Term] id: MI:0046 name: experimental knowledge based def: "Predictive algorithms that rely on the information obtained by experimental results." [PMID:14755292] subset: PSI-MI_slim synonym: "experimental info" EXACT PSI-MI-short [] is_a: MI:0063 ! interaction prediction [Term] id: MI:0047 name: far western blotting def: "Proteins are fractionated by PAGE (SDS-polyacrylamide gel electrophoresis), transferred to a nitrocellulose membrane and tested for the ability to bind to a protein, a peptide, or any other ligand. Cell lysates can also be fractionated before gel electrophoresis to increase the sensitivity of the method for detecting interactions with rare proteins. Denaturants are removed during the blotting procedure, which allows many proteins to recover (or partially recover) activity. However, if biological activity is not recoverable, the proteins can be fractionated by a non denaturing gel system. This variation of the method eliminates the problem of activity regeneration and allows the detection of binding when the presence of a protein complex is required for binding. The protein probe can be prepared by any one of several procedures, while fusion affinity tags greatly facilitate purification. Synthesis in E. coli with a GST fusion, epitope tag, or other affinity tag is most commonly used. The protein of interest can then be radioactively labelled, biotinylated, or used in the blotting procedure as an unlabeled probe that is detected by a specific antibody." [PMID:7708014] subset: PSI-MI_slim synonym: "Affinity blotting" EXACT PSI-MI-alternate [] is_a: MI:0892 ! solid phase assay [Term] id: MI:0048 name: filamentous phage display def: "Filamentous phages (M13, f1, fd) have been extensively used to develop and implement the technology of phage display. Repertoires of relatively short peptides of random amino acid sequences or cDNA libraries have been constructed and searched successfully. Most experiments have taken advantage of the ability to assemble phages decorated with hybrid versions of the receptor protein pIII or of the major coat protein pVIII. Both systems allow the display of foreign peptides by fusion to the amino-terminus of the capsid protein but differ in the number of peptide copies that can be displayed on each phage particle. Display libraries of very diverse protein fragments have been constructed by fusing either genomic or cDNA fragments to gene III or gene VIII." [PMID:7682645] subset: PSI-MI_slim synonym: "filamentous phage" EXACT PSI-MI-short [] is_a: MI:0084 ! phage display [Term] id: MI:0049 name: filter binding def: "A method in which separation depends upon the ability of one participant to bind to a filter or membrane which the other participants do not. Molecules interacting with the bound molecule will also be retain on the filter. For example, proteins expressed by different clones of an expression library are bound to a nitrocellulose membrane, by colony (bacterial library) or plaque (phage library) blotting. A labelled protein can then be used as a probe to identify clones expressing proteins that interact with the probe. Interactions occur on the nitrocellulose filters. The method is highly general and therefore widely applicable. A variety of approaches can be used to label the ligand, alternatively the ligand can be detected by a specific antibody." [PMID:7708014] subset: PSI-MI_slim synonym: "dot blot" RELATED [] synonym: "Filter overlay assay" EXACT PSI-MI-alternate [] is_a: MI:0892 ! solid phase assay [Term] id: MI:0050 name: flag tag coimmunoprecipitation def: "The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.\nOBSOLETE redundant term. Map to feature type: flag-tagged (MI:0518) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007)." [PMID:14755292] subset: PSI-MI_slim synonym: "flag tag coip" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0051 name: fluorescence technology def: "Techniques based upon the measurement of the emission of one or more photons by a molecule activated by the absorption of a quantum of electro-magnetic radiation. Typically the emission, which is characterised by a wavelength that is longer than the one of excitatory radiation, occurs within 10-8 seconds." [PMID:14755292] subset: PSI-MI_slim synonym: "fluorescence" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical [Term] id: MI:0052 name: fluorescence correlation spectroscopy def: "FCS monitors the random motion of fluorescently labelled molecules inside a defined volume irradiated by a focused laser beam. These fluctuations provide information on the rate of diffusion or diffusion time of a particle and this is directly dependent on the particle mass. As a consequence, any increase in the mass of a biomolecule, e.g. as a result of an interaction with a second molecule, is readily detected as an increase in the diffusion time of the particle. From these results the concentration of the different molecules can be calculated as well as their binding constant." [PMID:10733953] subset: PSI-MI_slim synonym: "FCS" EXACT PSI-MI-alternate [] synonym: "fcs" EXACT PSI-MI-short [] synonym: "fluctuation correlation specctrometry" RELATED [] is_a: MI:0051 ! fluorescence technology [Term] id: MI:0053 name: fluorescence polarization spectroscopy def: "Because of the long lifetimes of excited fluorescent molecules (nanoseconds), fluorescence can be used to monitor the rotational motion of molecules, which occurs on this timescale. This is accomplished experimentally by excitation with plane-polarized light, followed by measurement of the emission at parallel and perpendicular planes. Since rotational correlation times depend on the size of the molecule, this method can be used to measure the binding of two proteins because the observed polarization increase when a larger complex is formed. A fluorescence anisotropy experiment is normally carried out with a protein bearing a covalently added fluorescent group, which increases both the observed fluorescence lifetime of the excited state and the intensity of the fluorescent signal. Residue modification can be assessed by addition of an antibody which binds to the modified residue and alters the molecular weight of the complex. A variation of this technique has been used to show interaction of a DNA binding protein with another protein. In this case the DNA rather than protein is fluorescently labelled." [PMID:12805227, PMID:7708014] subset: PSI-MI_slim synonym: "Fluorescence anisotropy" EXACT PSI-MI-alternate [] synonym: "FPS" EXACT PSI-MI-alternate [] synonym: "fps" EXACT PSI-MI-short [] is_a: MI:0051 ! fluorescence technology [Term] id: MI:0054 name: fluorescence-activated cell sorting def: "Cells in suspension flow through a laser beam, the scattered light or emitted fluorescence is measured, filtered and converted to digital values. Cells can be sorted according to their properties. Using flow cytometry, any fluorescent or light scattering experiment can be carried out on entire cells. With this instrument, interactions occurring either on cell surfaces or in any other subcellular location can be studied by using suitable fluorescent labels." [PMID:11988464] subset: PSI-MI_slim synonym: "FACS" EXACT PSI-MI-alternate [] synonym: "facs" EXACT PSI-MI-short [] synonym: "Flow cytometry" EXACT PSI-MI-alternate [] is_a: MI:0051 ! fluorescence technology [Term] id: MI:0055 name: fluorescent resonance energy transfer def: "FRET is a quantum mechanical process involving the radiationless transfer of energy from a donor fluorophore to an appropriately positioned acceptor fluorophore. The fluorophores are genetically fused to the protein in analysis and cotransfected. Three basic conditions must be fulfilled for FRET to occur between a donor molecule and acceptor molecule. First, the donor emission spectrum must significantly overlap the absorption spectrum of the acceptor. Second, the distance between the donor and acceptor fluorophores must fall within the range 20 to 100 Angstrom. Third, the donor and acceptor fluorophores must be in favourable orientations." [PMID:11558993] subset: PSI-MI_slim synonym: "FRET" EXACT PSI-MI-alternate [] synonym: "fret" EXACT PSI-MI-short [] synonym: "FRET analysis" EXACT PSI-MI-alternate [] synonym: "RET" EXACT PSI-MI-alternate [] is_a: MI:0051 ! fluorescence technology [Term] id: MI:0056 name: full identification by DNA sequencing def: "Sequencing occurs during the course of the experiment. DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. Thus far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger. This technique uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. However, new sequencing technologies such as Pyrosequencing are generating the majority of data." [PMID:14755292] subset: PSI-MI_slim synonym: "full dna sequence" EXACT PSI-MI-short [] is_a: MI:0078 ! nucleotide sequence identification is_a: MI:0659 ! experimental feature detection [Term] id: MI:0057 name: gene neighbourhood def: "Gene pairs that show a conserved topological neighbourhood in many prokaryotic genomes are considered by this approach to encode interacting or functionally related proteins. By measuring the physical distance of any given gene pair in different genomes, interacting partners are inferred." [PMID:9787636] subset: PSI-MI_slim is_a: MI:0058 ! genome based prediction [Term] id: MI:0058 name: genome based prediction def: "Methods that require fully sequenced genomes either because they are based on the comparison of genome topology or on the identification of orthologous sequences in different genomes." [PMID:14755292] subset: PSI-MI_slim synonym: "genome prediction" EXACT PSI-MI-short [] is_a: MI:0063 ! interaction prediction [Term] id: MI:0059 name: gst pull down def: "The bait protein is expressed and purified as a fusion to the glutathione S-tranferase protein. The bait protein is normally attached to a glutathione sepharose resin or alternatively to a support containing an anti-GST antibody.\nOBSOLETE redundant term. Map to feature type : gst-tagged (MI:0519) and Interaction detection method: pull down (MI:0096)." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0060 name: ha tag coimmunoprecipitation def: "The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available.\nOBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007)." [PMID:14755292] subset: PSI-MI_slim synonym: "ha tag coip" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0061 name: his pull down def: "The bait protein is expressed and purified fused to an amino or carboxyterminal tail containing a variable number of histidines. The bait protein is normally attached to a metal (usually nickel) resin.\nOBSOLETE redundant term. Map to feature type : his-tagged (MI:0521) and Interaction detection method: pull down (MI:0096)." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0062 name: his tag coimmunoprecipitation def: "The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies.\nOBSOLETE redundant term. Map to feature type: his-tagged (MI:0521) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007)." [PMID:14755292] subset: PSI-MI_slim synonym: "his tag coip" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0063 name: interaction prediction def: "Computational methods to predict an interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "in silico methods" EXACT PSI-MI-alternate [] synonym: "predicted interac" EXACT PSI-MI-short [] is_a: MI:0001 ! interaction detection method [Term] id: MI:0064 name: interologs mapping def: "Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties." [PMID:11731503] subset: PSI-MI_slim synonym: "Homology based interaction prediction" EXACT PSI-MI-alternate [] is_a: MI:0046 ! experimental knowledge based is_a: MI:0101 ! sequence based prediction [Term] id: MI:0065 name: isothermal titration calorimetry def: "Isothermal titration calorimetry (ITC) measures directly the energy associated with a chemical reaction triggered by the mixing of two components. A typical ITC experiment is carried out by the stepwise addition of one of the reactants (~10-6 L per injection) into the reaction cell (~1mL) containing the second reactant. The chemical reaction occurring after each injection either releases or absorbs heat (qi) proportional to the amount of ligand that binds to the protein with a characteristic binding enthalpy (DH). As modern ITC instruments operate on the heat compensation principle, the instrumental response (measured signal) is the amount of power (microcalories per second) necessary to maintain constant the temperature difference between the reaction and the reference cells. Because the amount of uncomplexed protein available progressively decreases after each successive injection, the magnitude of the peaks becomes progressively smaller until complete saturation is achieved. The difference between the concentration of bound ligand in the ith and (i-1)th injections depends on the binding constant Ka and the total ligand injected. The calculations depend on the binding model (number of substrates). Analysis of the data yields DH and DG = -RTlnKa. The entropy change is obtained by using the standard thermodynamic expression DG = DH-TDS." [PMID:11785756] subset: PSI-MI_slim synonym: "ITC" EXACT PSI-MI-alternate [] synonym: "itc" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical [Term] id: MI:0066 name: lambda phage display def: "Morphologically classified as one of the siphoviridae, lambda is a temperate bacteriophage of E.coli, with a double-stranded DNA genome. It has an icosahedral head attached to a flexible helical tail. Both the tail protein pV and the head protein pD have been used for displaying (C or N terminally) foreign peptides on the viral capsid." [PMID:7682645] subset: PSI-MI_slim synonym: "lambda phage" EXACT PSI-MI-short [] is_a: MI:0084 ! phage display [Term] id: MI:0067 name: light scattering def: "Dynamic and static laser light scattering probes the size, shape, and structure of biological macromolecules or of their assemblies. A beam is focused on an optically clear cylindrical cell containing the sample. Most of the light passes directly through the sample. A small portion of the light is scattered; the scattered light intensity containing information about the scattering particle is detected at an angle (typically in the range 15-180degrees) from the direction of the incident beam." [PMID:9013660] subset: PSI-MI_slim is_a: MI:0013 ! biophysical [Term] id: MI:0068 name: mass detection of residue modification def: "Mass spectrometry can be used to characterise chemical modifications within peptides. One approach consists in the observation of a mass difference when a sample is treated with an enzyme that can specifically remove a peptide modification, for instance a phosphatase. The mass difference corresponds to the mass of the chemical group covalently linked to a residue. Such experiments carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) do not allow the mapping of the modification site within the sequence, whereas any tandem mass spectrometer (LC MS/MS Liquid Chromatography Tandem Mass Spectrometry, nanoESI MS/MS nanoElectrospray Ionisation tandem mass spectrometry, FTMS Fourier Transform mass spectrometry) provide such information. A second approach consists of the direct mass measurement of the ionized chemical group dissociated from the residue within a tandem mass spectrometer. Both approaches need a prior enrichment of the modified peptide population in the samples with IMAC (Immobilized Metal Affinity Chromatography)or specific anti-modification antibodies." [PMID:11395414, PMID for application instance:11875433] subset: PSI-MI_slim synonym: "modified residue ms" EXACT PSI-MI-short [] is_a: MI:0659 ! experimental feature detection [Term] id: MI:0069 name: mass spectrometry studies of complexes def: "Mass spectrometric approaches to the study of macromolecular complexes permits the identification of subunit stoichiometry and transient associations. By preserving complexes intact in the mass spectrometer, mass measurement can be used for monitoring changes in different experimental conditions, or to investigate how variations of collision energy affect their dissociation." [PMID:12504676, PMID for application instance:12057199] subset: PSI-MI_slim synonym: "ms of complexes" EXACT PSI-MI-short [] is_a: MI:0943 ! detection by mass spectrometry [Term] id: MI:0070 name: mobility shift def: "Protein modifications can be identified by gel electrophoresis since any change in the mass and/or the charge of the protein can alter its mobility in PAGE. Although this method does not allow the unequivocal identification of the type of modification that has caused the shift, it is possible, by combining this approach with more direct methods, to correlate the extent of the shift to a specific modification." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0659 ! experimental feature detection [Term] id: MI:0071 name: molecular sieving def: "In sizing columns (gel filtration), the elution position of a protein or of a complex depends on its Stokes radius. Molecules with a radius that is smaller than the bead size are retained and retarded by the interaction with the matrix. The observation that two proteins, loaded on a sieving column, elute in a fraction(s) corresponding to a MW that is larger than the MW of either protein may be taken as an indication that the two proteins interact. Furthermore this technique provides a conceptually simple method for evaluating the affinity of the interaction." [PMID:7708014] subset: PSI-MI_slim synonym: "Gel Filtration" EXACT PSI-MI-alternate [] synonym: "Size Exclusion Chromatography" EXACT PSI-MI-alternate [] synonym: "Sizing column" EXACT PSI-MI-alternate [] is_a: MI:0013 ! biophysical is_a: MI:0091 ! chromatography technology [Term] id: MI:0072 name: monoclonal antibody western blot def: "Western blot assay carried out using monospecific antibodies produced in the supernatant of a cell line obtained by fusing a lymphocyte B to a myeloma cell line or selected by phage display technology." [PMID:14755292] subset: PSI-MI_slim synonym: "monoclonal western" EXACT PSI-MI-short [] is_a: MI:0113 ! western blot [Term] id: MI:0073 name: mrna display def: "This method relies on the covalent coupling of mRNA to the nascent polypeptide. The mRNA (natural or artificial) is first covalently linked to a short DNA linker carrying a puromycin moiety. The mRNA mixture is then translated in vitro. When the ribosome reaches the RNA-DNA junction the ribosome stalls and the puromycin moiety enters the peptidyltransferase site of the ribosome and forms a covalent linkage to the nascent polypeptide. As a result the protein and the mRNA are covalently joined and can be isolated from the ribosome and purified. In the current protocol, a cDNA strand is then synthesised to form a less sticky RNA-DNA hybrid and these complexes are finally used for affinity selection. As in most display approaches, several selections cycles (3-6) are sufficient to enrich for mRNAs encoding ligand proteins." [PMID:11551470] subset: PSI-MI_slim is_a: MI:0034 ! display technology [Term] id: MI:0074 name: mutation analysis def: "Mutant molecules are produced by random or directed techniques and assayed for their ability to support binding." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0659 ! experimental feature detection [Term] id: MI:0075 name: myc tag coimmunoprecipitation def: "The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.\nOBSOLETE redundant term. Map to feature type: myc-tagged (MI:0522) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007)." [PMID:14755292] subset: PSI-MI_slim synonym: "myc tag coip " EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0076 name: neural network on interface properties def: "Neural networks are trained on the properties of residues belonging to a cluster of residues that are neighbours in space on protein surface. The predictor permits the inference of the residues that are likely to be on an interaction interface." [PMID:11455607, PMID:11874449] subset: PSI-MI_slim synonym: "interface predictor" EXACT PSI-MI-short [] is_a: MI:0577 ! feature prediction from structure [Term] id: MI:0077 name: nuclear magnetic resonance def: "Nuclear magnetic resonance (NMR) is an effect whereby magnetic nuclei in a magnetic field absorb and re-emit electromagnetic (EM) energy. Certain atomic nuclei, and in particular hydrogen, have a magnetic moment or spin; i.e., they have an intrinsic magnetisation, like a bar magnet. The spin aligns along the strong magnetic field, but can be changed to a misaligned excited state in response to applied radio frequency (RF) pulses of electromagnetic radiation. When the excited hydrogen nuclei relax to their aligned state, they emit RF radiation, which can be measured and displayed as a spectrum. The nature of the emitted radiation depends on the environment of each hydrogen nucleus, and if one nucleus is excited, it will influence the absorption and emission of radiation by other nuclei that lie close to it. It is consequently possible, by an ingenious elaboration of the basic NMR technique known as two-dimensional NMR, to distinguish the signals from hydrogen nuclei in different amino acid residues and to identify and measure the small shifts in these signals that occur when these hydrogen nuclei lie close enough to interact: the size of such a shift reveals the distance between the interacting pair of hydrogen atoms. In this way NMR can give information about the distances between the parts of the interacting molecule. NMR provides information about interacting atoms thereby permitting to obtain information about macromolecular structure and molecular interactions." [PMID:12120505, PMID for application instance:12062432] subset: PSI-MI_slim synonym: "NMR" EXACT PSI-MI-alternate [] synonym: "nmr" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical is_a: MI:0659 ! experimental feature detection [Term] id: MI:0078 name: nucleotide sequence identification def: "Identification of a nucleotide sequence. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones." [PMID:14755292] subset: PSI-MI_slim synonym: "nucleotide sequence" EXACT PSI-MI-short [] synonym: "sequence cloning" EXACT PSI-MI-alternate [] is_a: MI:0659 ! experimental feature detection is_a: MI:0661 ! experimental participant identification [Term] id: MI:0079 name: other biochemical technologies def: "Experimental methods that could not be assigned to the other large group of technologies.\nOBSOLETE use biochemical (MI:0401) instead." [PMID:14755292] subset: PSI-MI_slim synonym: "other biochemic tech" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0080 name: partial DNA sequence identification by hybridization def: "Genes are recognised by hybridization of a probe with a fragment of the gene sequence." [PMID:14755292] subset: PSI-MI_slim synonym: "partial dna sequence hybrid" EXACT PSI-MI-short [] is_a: MI:1180 ! partial DNA sequence identification [Term] id: MI:0081 name: peptide array def: "The peptide synthesis methods offer numerous opportunities to synthesise and subsequently screen large arrays of synthetic peptides on planar cellulose supports. Discrete spots are arranged as arrays on membrane sheets where each spot is individually accessed by manual or automated delivery of the appropriate reagent solutions. Over the past few years protein-protein recognition, peptide-metal ion interactions, peptide-nucleic acid binding, enzymatic modification of peptides experiments, have been explored using synthetic peptide arrays on planar support." [PMID:11167074] subset: PSI-MI_slim is_a: MI:0008 ! array technology [Term] id: MI:0082 name: peptide massfingerprinting def: "This approach leads to protein identification by matching peptide masses, as measured by mass spectrometry, to the ones calculated from in silico fragmentation of a protein sequence database. A peptide mixture from a tryptic digest is analysed by MALDI-MS (Matrix-assisted laser desorption ionization mass spectrometry). The list of peptide masses obtained by MALDI MS is automatically compared to the calculated masses of the predicted peptide fragments for each entry in the database. High mass accuracy is very important in order to obtain a statistically significant and unambiguous match This method is best applied to completely sequenced genomes and well characterised proteomes. However, depending on the data quality, proteins that are highly homologous to already characterised proteins (greater than 80 to 90% sequence identity) can also be identified. The retrieved sequence are evaluated by mass accuracy of the peptides, matching of additional peptide masses in the MALDI spectrum after accounting for common modifications such as oxidation, acrylamidation of cysteine and missed cleavages and the use of secondary information (apparent isoelectric point and molecular weight). If any ambiguity about the identification by MALDI-MS still exists, the results must verified by an other identification method. Peptide mass fingerprint is generally carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) instrument but can also be achieved ESI-TOF (Electrospray Ionisation time-of-flight) or LC-MS (Liquid Chromatography-Mass Spectrometry) mass spectrometer." [PMID:10967324, PMID:11752590, PMID for application instance:11805826] subset: PSI-MI_slim synonym: "fingerprinting" EXACT PSI-MI-short [] is_a: MI:0427 ! Identification by mass spectrometry is_a: MI:0433 ! partial identification of protein sequence [Term] id: MI:0083 name: peptide synthesis def: "When one of the partners participates in the interaction with a relatively short peptide fragment, it is often convenient to precisely identify the minimal region that supports the interaction by synthesising a series of overlapping peptides and by testing them in the binding assay. Synthetic peptides that are identical with peptides synthesised in vivo are useful experimental tools for such studies. Peptides are routinely synthesised in a test tube from monomeric amino acids by condensation reactions that form peptide bonds. Peptides are constructed sequentially by coupling the C-terminus of a monomeric amino acid to the N-terminus of the growing peptide. To prevent unwanted reactions involving the amino groups and carboxyl groups of the side chains during the coupling steps, a protecting (blocking) group is attached to the side chains. Without these protecting groups, branched peptides would be generated. In the last steps of synthesis, the side chain-protecting groups are removed and the peptide is cleaved from the resin on which synthesis occurs." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0093 ! protein sequence identification [Term] id: MI:0084 name: phage display def: "Peptide sequences or entire proteins can be displayed on phage capsids by fusion to coat proteins to generate a library of fusion phages each displaying a different peptide. Such a library can then be exploited to identify specific phages that display peptides that bind to any given bait molecule for instance an antibody. The selection is performed by a series of cycles of affinity purification known as panning. The bait protein, immobilized on a solid support (plastic, agarose, sepharose, magnetic beads and others) is soaked in the phage mixture and that phage that remains attached to the bait is amplified and carried through a further affinity purification step. Each cycle results in an approximately 1,000-fold enrichment of specific phage and after a few selection rounds (2-4), DNA sequencing of the tight-binding phage reveals only a small number of sequences. Phage display panning experiments can be carried out either on libraries of peptides of random amino acid sequence or on libraries of displaying natural peptides obtained by inserting cDNA fragments into the phage vector (cDNA libraries). Libraries have been assembled on several different phages (Fd, Lambda or T7)." [PMID:10975452, PMID:7708014] subset: PSI-MI_slim is_a: MI:0034 ! display technology [Term] id: MI:0085 name: phylogenetic profile def: "The phylogenetic profile of a protein stores information about the presence and the absence of that protein in a set of genomes. By clustering identical or similar profiles, proteins with similar functions and potentially interacting are identified." [PMID:10200254] subset: PSI-MI_slim is_a: MI:0058 ! genome based prediction [Term] id: MI:0086 name: polyclonal antibody western blot def: "Western blot assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest." [PMID:14755292] subset: PSI-MI_slim synonym: "polyclonal western" EXACT PSI-MI-short [] is_a: MI:0113 ! western blot [Term] id: MI:0087 name: predictive text mining def: "Methods based on natural language processing to detect possible interactions between proteins (direct physical interactions or indirect genetic interactions). This includes the detection of non ambiguous protein or gene names and analysis of the relation expressed in a sentence among them." [PMID:11791231] subset: PSI-MI_slim synonym: "predictive tm" EXACT PSI-MI-short [] is_a: MI:0110 ! text mining [Term] id: MI:0088 name: primer specific pcr def: "Sequences can be identified in a DNA mixture by launching a PCR (Polymerase Chain Reaction) controlled by sequence specific primers. Such reaction starts only when the hybridization of the primer with a complementary sequence occurs." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0080 ! partial DNA sequence identification by hybridization [Term] id: MI:0089 name: protein array def: "The protein array technology allows the screening of biochemical activities or binding abilities of hundreds or thousands of protein samples in parallel. After synthesis and purification by high-throughput methodologies, the proteins are printed onto the chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with labelled molecules to identify proteins that bind to the bait." [PMID:10976071, PMID:12067604] subset: PSI-MI_slim is_a: MI:0008 ! array technology [Term] id: MI:0090 name: protein complementation assay def: "In the protein-fragment complementation assay, the proteins of interest (\"Bait\" and \"Prey\") are covalently linked at the genetic level to incomplete fragments of a third protein (known as the \"reporter\") and are expressed in vivo, Interaction between the \"bait\" and the \"prey\" proteins brings the fragments of the \"reporter\" protein in close enough proximity to allow them to reform and become the functional reporter protein. Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode." [PMID:11495741] subset: PSI-MI_slim synonym: "complementation" EXACT PSI-MI-short [] synonym: "PCA" EXACT PSI-MI-alternate [] is_a: MI:0045 ! experimental interaction detection [Term] id: MI:0091 name: chromatography technology def: "Used to separate and/or analyse complex mixtures. The components to be separated are distributed between two phases: a stationary phase (bed) and a mobile phase which percolates through the stationary bed. The nature of the two phases determines the separation criteria exploited by the column such as affinity, ionic charges, size or hydrophobicity of the molecules under analysis. Each type of column can be implemented with the mobile phase under atmospheric or high pressure condition. In this later case columns are designated as High Pressure Liquid Chromatography (HPLC)." [PMID:14755292] subset: PSI-MI_slim synonym: "chromatography" EXACT PSI-MI-short [] synonym: "column chromatography" EXACT PSI-MI-alternate [] is_a: MI:0401 ! biochemical [Term] id: MI:0092 name: protein in situ array def: "Protein In Situ Array is a method by which protein arrays are rapidly generated in one step directly from DNA, by cell-free protein expression and simultaneous in situ immobilisation at a surface. Individual genes or fragments are produce by PCR or RT-PCR depending on the source of genetic material using properly designed primers. The PISA is generated by cell-free protein synthesis using coupled transcription and translation to produce a tagged protein, the reaction being carried out on a surface to which the protein adheres as soon as it is synthesised." [PMID:11470888] subset: PSI-MI_slim synonym: "PISA" EXACT PSI-MI-alternate [] synonym: "pisa" EXACT PSI-MI-short [] is_a: MI:0089 ! protein array [Term] id: MI:0093 name: protein sequence identification def: "Single amino acid identification along a protein sequence." [PMID:14755292] subset: PSI-MI_slim synonym: "protein sequence" EXACT PSI-MI-short [] is_a: MI:0661 ! experimental participant identification [Term] id: MI:0094 name: protein staining def: "A wide range of dyes have been used over the years to visualise proteins in polyacrylamide gels - Coomasie Blue and silver-staining being two classical methods. Fluorescent dyes such as Nile Red and SYPRO Orange are now increasingly used due to their superior dynamic range. Use of non-denaturing gels can allow visualisation of protein protein interactions. Several dyes can be used to specifically indicate residue modification, however this methodology will give no information as the number of residues modified or their position within the protein sequence. Examples include the use of acid fuscian or the fluorescent dansyl hydrazine to show protein glycosylation." [PMID:12015990] subset: PSI-MI_slim is_a: MI:0659 ! experimental feature detection [Term] id: MI:0095 name: proteinchip(r) on a surface-enhanced laser desorption/ionization def: "ProteinChip(r) Array technology is a surface-enhanced laser desorption/ionization (SELDI) approach (Ciphergen Biosystems Inc. Fremont, CA, USA) for sample fractionation accomplished by retentate chromatography. Retentate chromatography is performed on ProteinChip Arrays with varying chromatographic properties (e.g. anion exchange, cation exchange, metal affinity and reverse phase). By utilising arrays with differing surface chemistries in parallel and in series, a complex mixture of proteins, as from cells or body fluids, can be resolved into subsets of proteins with common properties. Specific analytes can also be examined by using preactivated arrays to which a bait molecule (such as an antibody or biotinylated DNA) is immobilized and a solution containing the binding partner(s) is presented to the array. This array-based immunoprecipitation or protein-binding experiment has been used with good success to study DNA-binding proteins, receptor-ligand interactions, and protein complexes. Any ligand retained on a SELDI chip can directly be identified by mass spectrometry." [PMID:11827829] subset: PSI-MI_slim synonym: "seldi chip" EXACT PSI-MI-short [] synonym: "SELDI ProteinChip" EXACT PSI-MI-alternate [] is_a: MI:0089 ! protein array [Term] id: MI:0096 name: pull down def: "A specific affinity chromatography method where a molecule of interest (bait) is bound to a column, often via an affinity tag expressed as a protein fusion (GST, HIS tag and others) or chemically linked to the bait molecule . The molecule may be expressed or synthesised and purified first, often in an heterologous system, bound to the matrix at high concentration and then challenged with a solution or cellular extract containing the candidate partner molecules. Alternatively, a multi-molecular complex may be adsorbed to the resin and the retained binding molecules subsequently identified." [PMID:14755292] subset: PSI-MI_slim synonym: "affinity capture" RELATED [] synonym: "pulldown" RELATED [] is_a: MI:0004 ! affinity chromatography technology [Term] id: MI:0097 name: reverse ras recruitment system def: "In this complementation approach the bait can be any membrane protein (for example a receptor or a channel protein), the prey is cloned as a fusion protein of any cDNA from a library and the coding sequence of cytoplasmic RAS (cdc25 in yeast). If the bait and the prey interact, RAS is recruited close to the membrane and can activate cell growth. This procedure must take place in cells having a mutated RAS (Cdc25-2 yeast strain having a temperature sensitive mutation of RAS) to avoid constitutive growth activation." [PMID:11160938] subset: PSI-MI_slim synonym: "reverse RRS" EXACT PSI-MI-alternate [] synonym: "reverse rrs" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0098 name: ribosome display def: "This method permits the coupling of phenotype to genotype via the formation of a non-covalent ternary complex between mRNAs and their encoded polypeptides while they are translated in an in vitro system. As a first step a cDNA library is constructed that encodes chimeric proteins in which the natural proteins or protein domains are fused to a C-terminal tether. As a consequence when the mRNA is translated in vitro the domain can fold while the tether is still in the ribosomal tunnel. Furthermore this chimeric mRNAs lack a stop codon, thus preventing release of the mRNA and the polypeptide from the ribosome. High concentrations of magnesium and low temperature further stabilise the ternary complex. Similarly to phage display, these complexes can be used directly to select for nucleic acids encoding proteins with desired properties." [PMID:11551470, PMID for application instance:12167034] subset: PSI-MI_slim is_a: MI:0034 ! display technology [Term] id: MI:0099 name: scintillation proximity assay def: "SPA relies upon the fact that a beta particle emitted from a radioisotope decay can excite a fluorophore only when it is at a very short distance in water solution (few micrometers). The ligand is labelled with a radioactive atom and its potential partner is fixed to fluorophore containing beads, the emitted fluorescence proving their interaction can be measured in a scintillation counter. The scintillator measures only the amount of bound radiolabelled ligand. Competition experiment with cold competitor can be done to estimate the binding affinities (50% inhibitory concentration [IC50], cold ligand versus labelled ligand). Loss of signal can also be used to measure substrate cleavage by an enzyme, and labelled antibodies used to titrate the degree of modified residue present." [PMID:3866247] subset: PSI-MI_slim synonym: "RIA Radio Immuno Assay" EXACT PSI-MI-alternate [] synonym: "SPA" EXACT PSI-MI-alternate [] synonym: "spa" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical [Term] id: MI:0100 name: sequence based phylogenetic profile def: "Multiple alignments of orthologous sequences in the same species and their corresponding phylogenetic trees are built. Every phylogenetic tree is computed as a matrix of distances between all possible interacting pairs. The covariation of the distance matrices reveals interacting pairs." [PMID:11707606] subset: PSI-MI_slim synonym: "sequence phylogeny" EXACT PSI-MI-short [] is_a: MI:0058 ! genome based prediction is_a: MI:0101 ! sequence based prediction [Term] id: MI:0101 name: sequence based prediction def: "Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs." [PMID:14755292] subset: PSI-MI_slim synonym: "predict from sequenc" EXACT PSI-MI-short [] is_a: MI:0063 ! interaction prediction [Term] id: MI:0102 name: sequence tag identification def: "This approach leads to protein identification by combining mass measurement and short amino acid sequence information obtained by tandem mass spectrometry. This information is then used to automatically find the best match in a sequence database. A mixture of peptides derived from a protease digestion is analysed by nanoelectrospray LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometer or nanoESI MS/MS) mass spectrometry. Electrospray mass spectrometry cannot be applied to dilute samples and is affected by high salt. As a consequence peptides, normally extracted from acrylamide gels by in situ proteolysis, are desalted and concentrated on a microcolumn followed by elution into a capillary used for nanoelectrospray tandem mass spectrometry. A first mass spectrum (Normal mass spectrum or Q1 mass spectrum) gives information about the masses of all the peptides. Peptides observed in the normal mass spectrum are isolated in turn and dissociated into fragments by collision with gas molecules within the mass spectrometer. Some of the fragments obtained from a peptide constitute a nested set, differing by one amino acid, and the mass difference between them allows assignment of a partial sequence. The masses of the fragments define the position of the partial sequence in the peptide. Together with the cleavage specificity of the protease used to cleave the protein, and mass information such sequence tag provides much higher search specificity to match the a database entry. The procedure is repeated with several peptides from the digest, resulting in multiple identifications of the same protein or identification of several proteins from the peptide mixture. Unknown proteins can easily be identified by using the high specificity of the peptide sequence tag for searches in most sequence databases including EST or genome databases." [PMID:10967324, PMID:11752590, PMID for application instance:11805837] subset: PSI-MI_slim synonym: "MS/MS" RELATED [] synonym: "sequence tag" EXACT PSI-MI-short [] is_a: MI:0427 ! Identification by mass spectrometry is_a: MI:0433 ! partial identification of protein sequence [Term] id: MI:0103 name: southern blot def: "A standard procedure to identify DNA fragments containing specific gene sequences. In this procedure i) a genome is fragmented using a restriction enzyme ii) the generated fragments are separated by electrophoresis iii) the fragments are transferred to a membrane iv)the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0080 ! partial DNA sequence identification by hybridization [Term] id: MI:0104 name: static light scattering def: "In static light scattering, the average intensity of scattered light at multiple angles is measured. The data yield information on particle molecular weight, particle size and shape, and particle-particle interactions." [PMID:9013660] subset: PSI-MI_slim synonym: "sls" EXACT PSI-MI-short [] is_a: MI:0067 ! light scattering [Term] id: MI:0105 name: structure based prediction def: "Methods based on 3D structure information." [PMID:14755292] subset: PSI-MI_slim synonym: "predict from struct" EXACT PSI-MI-short [] is_a: MI:0063 ! interaction prediction [Term] id: MI:0106 name: surface patches def: "Surface patches are built using 6 criteria: solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion and accessible surface area. Protein structures having similar patches are likely to have the same interactions." [PMID:9299343] subset: PSI-MI_slim is_a: MI:0577 ! feature prediction from structure [Term] id: MI:0107 name: surface plasmon resonance def: "This method measures formation of complex by monitoring changes in the resonance angle of light impinging on a gold surface as a result of changes in the refractive index of the surface. A ligand of interest (small molecule, peptide, protein, sugar, lipid, nucleic acid) is immobilized on a gold surface, and the interacting partner is injected in buffer flow over it. Biomolecules that interact with the immobilized ligand are retained on the surface, and alter the resonance angle of impinging light as a result of the change in refractive index brought about by the increased biomolecule mass retained on the surface. Since all the biomolecules belonging to the same class have the same refractive index and since there is a linear correlation between resonance angle shift and biomolecule concentration near the surface, this allows one to measure changes in concentration at the surface as a consequence of interaction. Furthermore, this is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation." [PMID:11896282, PMID:12120258, PMID:16338355] subset: PSI-MI_slim synonym: "BIAcore(r)" EXACT PSI-MI-alternate [] synonym: "Optical biosensor" EXACT PSI-MI-alternate [] synonym: "spr" EXACT PSI-MI-short [] is_a: MI:0659 ! experimental feature detection is_a: MI:0968 ! biosensor [Term] id: MI:0108 name: t7 phage display def: "T7 is a double stranded DNA bacteriophage with a thin-walled icosahedral capsid, ~550 Angstrom in diameter, which is decorated by 415 copies of the capsid protein, the product of gene 10. gp10 can tolerate insertions at the carboxyterminus without loosing its ability to be inserted into functional phage capsids. Both low density and high density display (albeit only with short peptides) can be achieved." [PMID:14755292] comment: Reference not index in medline: Rosenberg, A, Griffin, K, Studier, WS, McCormick, M, Berg, J, Novy, R, Mierendorf, R inNovations, 1996, 6, 1. subset: PSI-MI_slim synonym: "t7 phage" EXACT PSI-MI-short [] is_a: MI:0084 ! phage display [Term] id: MI:0109 name: tap tag coimmunoprecipitation def: "The TAP method involves the fusion of the TAP tag (encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A) to the target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This two steps purification steps ensures a highly selective complex purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag).\nOBSOLETE redundant term. Map to feature type: tap tagged (MI:0524) and as interaction detection method tandem affinity purification (MI:0676)." [PMID:10504710] subset: PSI-MI_slim synonym: "tap tag coip" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0110 name: text mining def: "Text mining methods can be used to predict or confirm interactions by automated processing of scientific literature. Co-occurrence in the same sentence of an abstract of gene products labels are analysed to evaluate whether it represents a valid evidence of an interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0046 ! experimental knowledge based [Term] id: MI:0111 name: dihydrofolate reductase reconstruction def: "The gene for DHFR is rationally dissected into two fragments called F[1,2] and F[3]. Two proteins or protein domains that are thought to bind to each other can then be fused to either of the two DHFR fragments. Reconstitution of enzyme activity can be monitored in vivo by cell survival in DHFR-negative cells grown in the absence of nucleotides. A fluorescence assay can also be carried out taking advantage of fMTX binding to reconstituted DHFR. The basis of this assay is that complementary fragments of DHFR, when expressed and reassembled in cells, will bind with high affinity (Kd 5 540 pM) to fMTX in a 1:1 complex. fMTX is retained in cells by this complex, whereas the unbound fMTX is actively and rapidly transported out of the cells. Survival depends only on the number of molecules of DHFR reassembled." [PMID:10318894] subset: PSI-MI_slim synonym: "dhfr reconstruction" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0112 name: ubiquitin reconstruction def: "The split-ubiquitin system provides a method for examining the interactions of membrane proteins. In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety (\"Cub\", residues 35-76) and an N-terminal ubiquitin moiety (\"Nub\", residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases. Upon bait-prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes." [PMID:9560251] subset: PSI-MI_slim synonym: "membrane yeast two-hybrid" RELATED [] synonym: "myth" RELATED [] synonym: "split-ubiquitin" RELATED [] synonym: "ub reconstruction" EXACT PSI-MI-short [] is_a: MI:1320 ! membrane yeast two hybrid [Term] id: MI:0113 name: western blot def: "Western blot is a procedure to identify and quantify proteins. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane." [PMID:14755292] subset: PSI-MI_slim synonym: "Immuno blot" EXACT PSI-MI-alternate [] is_a: MI:0421 ! identification by antibody is_a: MI:0659 ! experimental feature detection [Term] id: MI:0114 name: x-ray crystallography def: "Analysis of a diffraction pattern generated by a single crystal. X-rays have a wavelength, typically around 1 Angstrom (the diameter of a hydrogen atom). If a narrow parallel beam of X-rays is directed at a sample of a pure protein, most of the X-rays will pass straight through it. A small fraction, however, will be scattered by the atoms in the sample. If the sample is a well-ordered crystal, the scattered waves will reinforce one another at certain points and will appear as diffraction spots when the X-rays are recorded by a suitable detector. The position and intensity of each spot in the X-ray diffraction pattern contain information about the position and nature of the atoms in the crystal. The three-dimensional structure of a large molecule can be deduced from the electron-density map of its crystal. In recent years X-ray diffraction analysis has become increasingly automated, and now the slowest step is likely to be the production of suitable macromolecule crystals. This requires high concentration of very pure macromolecule and empirical searching for the proper crystallization conditions." [PMID:14755292] subset: PSI-MI_slim synonym: "co-crystallization" RELATED [] synonym: "co-crystallography" RELATED [] synonym: "X-ray" EXACT PSI-MI-alternate [] synonym: "x-ray diffraction" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical is_a: MI:0659 ! experimental feature detection [Term] id: MI:0115 name: yeast display def: "The proteins are displayed on the surface of the yeast S. cerevisiae by fusion to signal sequences for protein secretion. This method is limited by the low efficiency of the yeast display system but can take full advantage of exploiting cell sorting methods (FACS) to isolate cells that display molecules with desired binding properties." [PMID:9181578] subset: PSI-MI_slim is_a: MI:0034 ! display technology is_a: MI:0054 ! fluorescence-activated cell sorting [Term] id: MI:0116 name: feature type def: "Property of a subsequence that may interfere with the binding of a molecule." [PMID:14755292] subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0117 name: binding-associated region def: "A region of a molecule or a component of a complex identified as being involved in an interaction. This may or may not be a region of the molecule in direct contact with the interacting partner." [PMID:14755292] subset: PSI-MI_slim synonym: "binding component" RELATED [] synonym: "binding region" EXACT PSI-MI-short [] synonym: "binding site" BROAD [] is_a: MI:0252 ! biological feature [Term] id: MI:0118 name: mutation def: "A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0252 ! biological feature [Term] id: MI:0119 name: mutation decreasing interaction def: "Region of a molecule whose mutation or deletion decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction)." [PMID:14755292] subset: PSI-MI_slim synonym: "hotspot" EXACT PSI-MI-alternate [] synonym: "mutation decreasing" EXACT PSI-MI-short [] is_a: MI:0118 ! mutation [Term] id: MI:0120 name: post translation modification def: "Residue covalent modifications occurring in the specific protein form involved in an interaction.\nOBSOLETE remap to MOD:00000." [PMID:14755292] synonym: "ptm" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0121 name: acetylated residue def: "Residue modification.\nOBSOLETE remap to MOD:00394." [PMID:11125103] is_obsolete: true [Term] id: MI:0122 name: n-acetyl-alanine def: "Residue modification.\nOBSOLETE remap to MOD:00050." [PMID:11125103, RESID:AA0041] synonym: "(S)-2-(acetylamino)propanoic acid" EXACT PSI-MI-alternate [] synonym: "[A:ac]" EXACT PSI-MI-alternate [] synonym: "AAC" EXACT PSI-MI-alternate [] synonym: "acetylalanine" EXACT PSI-MI-alternate [] synonym: "acetylalanine" EXACT PSI-MI-short [] synonym: "N-acetyl-L-alanine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0123 name: n2-acetyl-arginine def: "Residue modification.\nOBSOLETE remap to MOD:00359." [PMID:11125103, RESID:AA0354] synonym: "[R:ac]" EXACT PSI-MI-alternate [] synonym: "acetylarginine" EXACT PSI-MI-alternate [] synonym: "acetylarginine" EXACT PSI-MI-short [] synonym: "alpha-acetylamino-delta-guanidinovaleric acid" EXACT PSI-MI-alternate [] synonym: "N2-acetyl-L-arginine" EXACT PSI-MI-alternate [] synonym: "RAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0124 name: n-acetyl-asparagine def: "Residue modification.\nOBSOLETE remap to MOD:00780." [PMID:11125103] synonym: "[N:ac]" EXACT PSI-MI-alternate [] synonym: "acetylasparagine" EXACT PSI-MI-short [] synonym: "N-acetyl-L-asparagine" EXACT PSI-MI-alternate [] synonym: "NAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0125 name: n-acetyl-aspartic acid def: "Residue modification.\nOBSOLETE remap to MOD:00051." [PMID:11125103, RESID:AA0042] synonym: "(S)-2-(acetylamino)butanedioic acid" EXACT PSI-MI-alternate [] synonym: "[D:ac]" EXACT PSI-MI-alternate [] synonym: "acetylaspartate" EXACT PSI-MI-short [] synonym: "acetylaspartic acid" EXACT PSI-MI-alternate [] synonym: "DAC" EXACT PSI-MI-alternate [] synonym: "N-acetyl-L-aspartic acid" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0126 name: n-acetyl-cysteine def: "Residue modification.\nOBSOLETE remap to MOD:00052." [PMID:11125103, RESID:AA0043] synonym: "(R)-2-acetylamino-3-sulfanylpropanoic acid" EXACT PSI-MI-alternate [] synonym: "2-acetylamino-3-mercaptopropanoic acid" EXACT PSI-MI-alternate [] synonym: "[C:ac]" EXACT PSI-MI-alternate [] synonym: "acetylcysteine" EXACT PSI-MI-short [] synonym: "CAC" EXACT PSI-MI-alternate [] synonym: "N-acetyl-L-cysteine" EXACT PSI-MI-alternate [] synonym: "N-acetylcysteine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0127 name: n-acetyl-glutamine def: "Residue modification.\nOBSOLETE remap to MOD:00054." [PMID:11125103, RESID:AA0045] synonym: "(S)-2-acetylamino-5-pentanediamic acid" EXACT PSI-MI-alternate [] synonym: "[Q:ac]" EXACT PSI-MI-alternate [] synonym: "acetylglutamine" EXACT PSI-MI-alternate [] synonym: "acetylglutamine" EXACT PSI-MI-short [] synonym: "N-acetyl-L-glutamine" EXACT PSI-MI-alternate [] synonym: "QAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0128 name: n-acetyl-glutamic acid def: "Residue modification.\nOBSOLETE remap to MOD:00053." [PMID:11125103, RESID:AA0044] synonym: "(S)-2-(acetylamino)pentanedioic acid" EXACT PSI-MI-alternate [] synonym: "[E:ac]" EXACT PSI-MI-alternate [] synonym: "acetylglutamate" EXACT PSI-MI-short [] synonym: "acetylglutamic acid" EXACT PSI-MI-alternate [] synonym: "EAC" EXACT PSI-MI-alternate [] synonym: "N-acetyl-L-glutamic acid" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0129 name: n-acetylglycine def: "Residue modification.\nOBSOLETE remap to MOD:00055." [PMID:11125103, RESID:AA0046] synonym: "2-(acetylamino)ethanoic acid" EXACT PSI-MI-alternate [] synonym: "[G:ac]" EXACT PSI-MI-alternate [] synonym: "aceturic acid" EXACT PSI-MI-alternate [] synonym: "acetylglycine" EXACT PSI-MI-short [] synonym: "GAC" EXACT PSI-MI-alternate [] synonym: "N-acetylglycine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0130 name: n-acetyl-histidine def: "Residue modification.\nOBSOLETE remap to MOD:00781." [PMID:11125103] synonym: "[H:ac]" EXACT PSI-MI-alternate [] synonym: "acetylhistidine" EXACT PSI-MI-short [] synonym: "HAC" EXACT PSI-MI-alternate [] synonym: "N-acetyl-L-histidine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0131 name: n-acetyl-isoleucine def: "Residue modification.\nOBSOLETE remap to MOD:00056." [PMID:11125103, RESID:AA0047] synonym: "(2S,3S)-2-acetylamino-3-methylpentanoic acid" EXACT PSI-MI-alternate [] synonym: "[I:ac]" EXACT PSI-MI-alternate [] synonym: "acetylisoleucine" EXACT PSI-MI-alternate [] synonym: "acetylisoleucine" EXACT PSI-MI-short [] synonym: "IAC" EXACT PSI-MI-alternate [] synonym: "N-acetyl-L-isoleucine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0132 name: n-acetyl-leucine def: "Residue modification.\nOBSOLETE remap to MOD:00782." [PMID:11125103] synonym: "[L:ac]" EXACT PSI-MI-alternate [] synonym: "acetylleucine" EXACT PSI-MI-short [] synonym: "LAC" EXACT PSI-MI-alternate [] synonym: "N-acetyl-L-leucine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0133 name: n2-acetyl-lysine def: "Residue modification.\nOBSOLETE remap to MOD:00057." [PMID:11125103, RESID:AA0048] synonym: "(S)-2-acetylamino-6-aminohexanoic acid" EXACT PSI-MI-alternate [] synonym: "[K:ac]" EXACT PSI-MI-alternate [] synonym: "KAC" EXACT PSI-MI-alternate [] synonym: "N2-acetyl-L-lysine" EXACT PSI-MI-alternate [] synonym: "N2-acetyllysine" EXACT PSI-MI-alternate [] synonym: "n2-acetyllysine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0134 name: n6-acetyl-lysine def: "Residue modification.\nOBSOLETE remap to MOD:00064." [PMID:11125103, RESID:AA0055] synonym: "(S)-2-amino-6-(acetylamino)hexanoic acid" EXACT PSI-MI-alternate [] synonym: "[K:N6ac]" EXACT PSI-MI-alternate [] synonym: "epsilon-acetyllysine" EXACT PSI-MI-alternate [] synonym: "KA6" EXACT PSI-MI-alternate [] synonym: "N(zeta)-acetyllysine" EXACT PSI-MI-alternate [] synonym: "N6-acetyl-L-lysine" EXACT PSI-MI-alternate [] synonym: "n6-acetyllysine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0135 name: n-acetyl-methionine def: "Residue modification.\nOBSOLETE remap to MOD:00058." [PMID:11125103, RESID:AA0049] synonym: "(S)-2-acetylamino-4-(methylsulfanyl)butanoic acid" EXACT PSI-MI-alternate [] synonym: "2-acetylamino-4-(methylthio)butanoic acid" EXACT PSI-MI-alternate [] synonym: "[M:ac]" EXACT PSI-MI-alternate [] synonym: "acetylmethionine" EXACT PSI-MI-alternate [] synonym: "acetylmethionine" EXACT PSI-MI-short [] synonym: "MAC" EXACT PSI-MI-alternate [] synonym: "methionamine" EXACT PSI-MI-alternate [] synonym: "N-acetyl-L-methionine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0136 name: n-acetyl-phenylalanine def: "Residue modification.\nOBSOLETE remap to MOD:00784." [PMID:11125103] synonym: "[F:ac]" EXACT PSI-MI-alternate [] synonym: "acetylphenylalanine" EXACT PSI-MI-short [] synonym: "FAC" EXACT PSI-MI-alternate [] synonym: "N-acetyl-L-phenylalanine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0137 name: n-acetyl-proline def: "Residue modification.\nOBSOLETE remap to MOD:00059." [PMID:11125103, RESID:AA0050] synonym: "(2S)-1-acetyl-2-pyrrolidinecarboxylic acid" EXACT PSI-MI-alternate [] synonym: "[P:ac]" EXACT PSI-MI-alternate [] synonym: "acetylproline" EXACT PSI-MI-alternate [] synonym: "acetylproline" EXACT PSI-MI-short [] synonym: "N-acetyl-L-proline" EXACT PSI-MI-alternate [] synonym: "PAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0138 name: n-acetyl-serine def: "Residue modification.\nOBSOLETE remap to MOD:00060." [PMID:11125103, RESID:AA0051] synonym: "(S)-2-acetylamino-3-hydroxypropanoic acid" EXACT PSI-MI-alternate [] synonym: "[S:ac]" EXACT PSI-MI-alternate [] synonym: "acetylserine" EXACT PSI-MI-short [] synonym: "N-acetyl-L-serine" EXACT PSI-MI-alternate [] synonym: "N-acetylserine" EXACT PSI-MI-alternate [] synonym: "SAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0139 name: n-acetyl-threonine def: "Residue modification.\nOBSOLETE remap to MOD:00061." [PMID:11125103, RESID:AA0052] synonym: "(2S,3R)-2-acetylamino-3-hydroxybutanoic acid" EXACT PSI-MI-alternate [] synonym: "[T:ac]" EXACT PSI-MI-alternate [] synonym: "acetylthreonine" EXACT PSI-MI-short [] synonym: "N-acetyl-L-threonine" EXACT PSI-MI-alternate [] synonym: "N-acetylthreonine" EXACT PSI-MI-alternate [] synonym: "TAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0140 name: n-acetyl-tryptophan def: "Residue modification.\nOBSOLETE remap to MOD:00785." [PMID:11125103] synonym: "[W:ac]" EXACT PSI-MI-alternate [] synonym: "acetyltryptophan" EXACT PSI-MI-short [] synonym: "N-acetyl-L-tryptophan" EXACT PSI-MI-alternate [] synonym: "WAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0141 name: n-acetyl-tyrosine def: "Residue modification.\nOBSOLETE remap to MOD:00062." [PMID:11125103, RESID:AA0053] synonym: "(S)-2-acetylamino-3-(4-hydoxyphenyl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "[Y:ac]" EXACT PSI-MI-alternate [] synonym: "acetyltyrosine" EXACT PSI-MI-short [] synonym: "N-acetyl-L-tyrosine" EXACT PSI-MI-alternate [] synonym: "N-acetyltyrosine" EXACT PSI-MI-alternate [] synonym: "YAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0142 name: n-acetyl-valine def: "Residue modification.\nOBSOLETE remap to MOD:00063." [PMID:11125103, RESID:AA0054] synonym: "(S)-2-acetylamino-3-methylbutanoic acid" EXACT PSI-MI-alternate [] synonym: "[V:ac]" EXACT PSI-MI-alternate [] synonym: "acetylvaline" EXACT PSI-MI-short [] synonym: "N-acetyl-L-valine" EXACT PSI-MI-alternate [] synonym: "N-acetylvaline" EXACT PSI-MI-alternate [] synonym: "VAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0143 name: amidated residue def: "Residue modification.\nOBSOLETE remap to MOD:00674." [PMID:11125103] is_obsolete: true [Term] id: MI:0145 name: arginine amide def: "Residue modification.\nOBSOLETE remap to MOD:00091." [PMID:11125103, RESID:AA0082] synonym: "(S)-2-amino-5-guanidinopentanamide" EXACT PSI-MI-alternate [] synonym: "[R:am]" EXACT PSI-MI-alternate [] synonym: "argininamide" EXACT PSI-MI-alternate [] synonym: "arginineamide" EXACT PSI-MI-short [] synonym: "L-arginine amide" EXACT PSI-MI-alternate [] synonym: "RAM" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0146 name: formylated residue def: "Residue modification.\nOBSOLETE remap to MOD:00493." [PMID:11125103] is_obsolete: true [Term] id: MI:0147 name: n-formyl-methionine def: "Residue modification.\nOBSOLETE remap to MOD:00030." [PMID:11125103, RESID:AA0021] synonym: "(S)-2-formylamino-4-(methylsulfanyl)butanoic acid" EXACT PSI-MI-alternate [] synonym: "2-formylamino-4-(methylthio)butanoic acid" EXACT PSI-MI-alternate [] synonym: "[M:form]" EXACT PSI-MI-alternate [] synonym: "formylmethionine" EXACT PSI-MI-short [] synonym: "MFM" EXACT PSI-MI-alternate [] synonym: "N-formyl-L-methionine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0148 name: hydroxylated residue def: "Residue modification.\nOBSOLETE remap to MOD:00428." [PMID:11125103] is_obsolete: true [Term] id: MI:0150 name: lipid modification def: "Residue modification.\nOBSOLETE remap to MOD:01155." [PMID:11125103] is_obsolete: true [Term] id: MI:0151 name: s-farnesyl-cysteine def: "Residue modification.\nOBSOLETE remap to MOD:00111." [PMID:11125103, RESID:AA0102] synonym: "(R,E,E)-2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylsulfanyl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid" EXACT PSI-MI-alternate [] synonym: "[C:farn]" EXACT PSI-MI-alternate [] synonym: "CFN" EXACT PSI-MI-alternate [] synonym: "farnesylcysteine" EXACT PSI-MI-short [] synonym: "S-farnesyl-L-cysteine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0152 name: s-geranylgeranyl-cysteine def: "Residue modification.\nOBSOLETE remap to MOD:00113." [PMID:11125103, RESID:AA0104] synonym: "(R,E,E,E)-2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylsulfanyl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid" EXACT PSI-MI-alternate [] synonym: "[C:ger]" EXACT PSI-MI-alternate [] synonym: "CGR" EXACT PSI-MI-alternate [] synonym: "geranylgeranylcys" EXACT PSI-MI-short [] synonym: "S-geranylgeranyl-L-cysteine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0153 name: n-palmitoyl-cysteine def: "Residue modification.\nOBSOLETE remap to MOD:00069." [PMID:11125103, RESID:AA0060] synonym: "(R)-2-hexadecanoylamino-3-sulfanylpropanoic acid" EXACT PSI-MI-alternate [] synonym: "2-hexadecanoylamino-3-mercaptopropanoic acid" EXACT PSI-MI-alternate [] synonym: "[C:palm_n]" EXACT PSI-MI-alternate [] synonym: "CPN" EXACT PSI-MI-alternate [] synonym: "N-(1-oxahexadecyl)-L-cysteine" EXACT PSI-MI-alternate [] synonym: "N-palmitoyl-L-cysteine" EXACT PSI-MI-alternate [] synonym: "n-palmitoylcysteine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0154 name: s-palmitoyl-cysteine def: "Residue modification.\nOBSOLETE remap to MOD:00115." [PMID:11125103, RESID:AA0106] synonym: "(R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-3-(hexadecanoylthio)propanoic acid" EXACT PSI-MI-alternate [] synonym: "[C:palm_s]" EXACT PSI-MI-alternate [] synonym: "CPS" EXACT PSI-MI-alternate [] synonym: "cysteine hexadecanoate thioester" EXACT PSI-MI-alternate [] synonym: "cysteine palmitate thioester" EXACT PSI-MI-alternate [] synonym: "S-palmitoyl-L-cysteine" EXACT PSI-MI-alternate [] synonym: "s-palmitoylcysteine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0155 name: n-myristoyl-glycine def: "Residue modification.\nOBSOLETE remap to MOD:00068." [PMID:11125103, RESID:AA0059] synonym: "[G:myr]" EXACT PSI-MI-alternate [] synonym: "GMY" EXACT PSI-MI-alternate [] synonym: "myristoylglycine" EXACT PSI-MI-short [] synonym: "N-myristoyl-glycine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0156 name: n6-myristoyl-lysine def: "Residue modification.\nOBSOLETE remap to MOD:00087." [PMID:11125103, RESID:AA0078] synonym: "(S)-2-amino-6-(tetradecanoylamino)hexanoic acid" EXACT PSI-MI-alternate [] synonym: "[K:myr]" EXACT PSI-MI-alternate [] synonym: "epsilon-myristoyllysine" EXACT PSI-MI-alternate [] synonym: "KMY" EXACT PSI-MI-alternate [] synonym: "myristoyllysine" EXACT PSI-MI-short [] synonym: "N(zeta)-myristoyllysine" EXACT PSI-MI-alternate [] synonym: "N6-(1-oxotetradecyl)-L-lysine" EXACT PSI-MI-alternate [] synonym: "N6-myristoyl-L-lysine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0157 name: methylated residue def: "Residue modification.\nOBSOLETE remap to MOD:00427." [PMID:11125103] is_obsolete: true [Term] id: MI:0158 name: n-methyl-alanine def: "Residue modification.\nOBSOLETE remap to MOD:00070." [PMID:11125103, RESID:AA0061] synonym: "(S)-2-methylaminopropanoic acid" EXACT PSI-MI-alternate [] synonym: "[A:meth_n]" EXACT PSI-MI-alternate [] synonym: "AMT" EXACT PSI-MI-alternate [] synonym: "methylalanine" EXACT PSI-MI-short [] synonym: "N-methyl-L-alanine" EXACT PSI-MI-alternate [] synonym: "N-methylalanine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0159 name: n,n,n-trimethyl-alanine def: "Residue modification.\nOBSOLETE remap to MOD:00071." [PMID:11125103, RESID:AA0062] synonym: "(S)-1-carboxy-N,N,N-trimethylethanaminium" EXACT PSI-MI-alternate [] synonym: "(S)-2-(trimethylammonio)propanoic acid" EXACT PSI-MI-alternate [] synonym: "[A:meth_n3]" EXACT PSI-MI-alternate [] synonym: "AM3" EXACT PSI-MI-alternate [] synonym: "N,N,N-trimethyl-L-alanine" EXACT PSI-MI-alternate [] synonym: "trimethylalanine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0160 name: omega-n,omega-n-dimethyl-arginine def: "Residue modification.\nOBSOLETE remap to MOD:00077." [PMID:11125103, RESID:AA0068] synonym: "(S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid" EXACT PSI-MI-alternate [] synonym: "[R:meth_n7]" EXACT PSI-MI-alternate [] synonym: "asymmetric dimethylarginine" EXACT PSI-MI-alternate [] synonym: "dimethylarginine" EXACT PSI-MI-short [] synonym: "NG,NG-dimethylarginine" EXACT PSI-MI-alternate [] synonym: "omega-N,omega-N-dimethyl-L-arginine" EXACT PSI-MI-alternate [] synonym: "RM2" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0161 name: beta-methylthioaspartic acid def: "Residue modification.\nOBSOLETE remap to MOD:00237." [PMID:11125103, RESID:AA0232] synonym: "(2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid" EXACT PSI-MI-alternate [] synonym: "3-carboxy-S-methyl-cysteine" EXACT PSI-MI-alternate [] synonym: "3-methylthio-aspartic acid" EXACT PSI-MI-alternate [] synonym: "[D:meth_b]" EXACT PSI-MI-alternate [] synonym: "beta-methylthio-aspartic acid" EXACT PSI-MI-alternate [] synonym: "DM2" EXACT PSI-MI-alternate [] synonym: "L-beta-methylthioaspartic acid" EXACT PSI-MI-alternate [] synonym: "methylthioaspartate" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0162 name: n5-methyl-glutamine def: "Residue modification.\nOBSOLETE remap to MOD:00080." [PMID:11125103, RESID:AA0071] synonym: "(S)-2-amino-N5-methylpentanediamic acid" EXACT PSI-MI-alternate [] synonym: "[Q:meth_n5]" EXACT PSI-MI-alternate [] synonym: "gamma-methylglutamine" EXACT PSI-MI-alternate [] synonym: "methylglutamine" EXACT PSI-MI-short [] synonym: "N(delta)-methylglutamine" EXACT PSI-MI-alternate [] synonym: "N-methylglutamine" EXACT PSI-MI-alternate [] synonym: "N5-methyl-L-glutamine" EXACT PSI-MI-alternate [] synonym: "QM5" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0163 name: glutamic acid 5-methyl ester def: "Residue modification.\nOBSOLETE remap to MOD:00081." [PMID:11125103, RESID:AA0072] synonym: "(S)-2-aminopentanedioic acid 5-methyl ester" EXACT PSI-MI-alternate [] synonym: "5-methyl-L-glutamate" EXACT PSI-MI-alternate [] synonym: "[E:meth_o5]" EXACT PSI-MI-alternate [] synonym: "EM5" EXACT PSI-MI-alternate [] synonym: "glutamatemethylester" EXACT PSI-MI-short [] synonym: "glutamic acid gamma-methyl ester" EXACT PSI-MI-alternate [] synonym: "L-glutamic acid 5-methyl ester" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0165 name: n6-methyl-lysine def: "Residue modification.\nOBSOLETE remap to MOD:00085." [PMID:11125103] synonym: "(S)-2-amino-6-methylaminohexanoic acid" EXACT PSI-MI-alternate [] synonym: "[K:meth_1]" EXACT PSI-MI-alternate [] synonym: "epsilon-methyllysine" EXACT PSI-MI-alternate [] synonym: "methyllysine" EXACT PSI-MI-short [] synonym: "MLZ" EXACT PSI-MI-alternate [] synonym: "N(zeta)-methyllysine" EXACT PSI-MI-alternate [] synonym: "N6-methyl-L-lysine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0166 name: n6,n6-dimethyl-lysine def: "Residue modification.\nOBSOLETE remap to MOD:00084." [PMID:11125103, RESID:AA0075] synonym: "(S)-2-amino-6-dimethylaminohexanoic acid" EXACT PSI-MI-alternate [] synonym: "[K:meth_2]" EXACT PSI-MI-alternate [] synonym: "dimethyllysine" EXACT PSI-MI-short [] synonym: "epsilon-dimethyllysine" EXACT PSI-MI-alternate [] synonym: "lysine derivative Lys(y)" EXACT PSI-MI-alternate [] synonym: "MLY" EXACT PSI-MI-alternate [] synonym: "N(zeta)-dimethyllysine" EXACT PSI-MI-alternate [] synonym: "N6,N6-dimethyl-L-lysine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0167 name: n6,n6,n6-trimethyl-lysine def: "Residue modification.\nOBSOLETE remap to MOD:00083." [PMID:11125103, RESID:AA0074] synonym: "(S)-2-amino-6-(trimethylammonio)hexanoic acid" EXACT PSI-MI-alternate [] synonym: "(S)-5-amino-5-carboxy-N,N,N-trimethylpentanaminium" EXACT PSI-MI-alternate [] synonym: "[K:meth_3]" EXACT PSI-MI-alternate [] synonym: "epsilon-trimethyllysine" EXACT PSI-MI-alternate [] synonym: "M3L" EXACT PSI-MI-alternate [] synonym: "N(zeta)-trimethyllysine" EXACT PSI-MI-alternate [] synonym: "N6,N6,N6-trimethyl-L-lysine" EXACT PSI-MI-alternate [] synonym: "trimethyllysine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0168 name: n-methyl-methionine def: "Residue modification.\nOBSOLETE remap to MOD:00073." [PMID:11125103, RESID:AA0064] synonym: "(S)-2-methylamino-4-(methylsulfanyl)butanoic acid" EXACT PSI-MI-alternate [] synonym: "2-methylamino-4-(methylthio)butanoic acid" EXACT PSI-MI-alternate [] synonym: "[M:meth]" EXACT PSI-MI-alternate [] synonym: "methylmethionine" EXACT PSI-MI-short [] synonym: "MMT" EXACT PSI-MI-alternate [] synonym: "N-methyl-L-methionine" EXACT PSI-MI-alternate [] synonym: "N-methylmethionine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0169 name: n-methyl-phenylalanine def: "Residue modification.\nOBSOLETE remap to MOD:00074." [PMID:14755292] synonym: "(S)-2-methylamino-3-phenylpropanoic acid" EXACT PSI-MI-alternate [] synonym: "[F:meth]" EXACT PSI-MI-alternate [] synonym: "FMT" EXACT PSI-MI-alternate [] synonym: "methylphenylalanine" EXACT PSI-MI-short [] synonym: "N-methyl-L-phenylalanine" EXACT PSI-MI-alternate [] synonym: "N-methylphenylalanine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0170 name: phosphorylated residue def: "Residue modification.\nOBSOLETE remap to MOD:00696." [PMID:11125103] synonym: "phosphorylated" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0171 name: omega-n-phospho-arginine def: "Residue modification.\nOBSOLETE remap to MOD:00227." [PMID:11125103, RESID:AA0222] synonym: "(S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid" EXACT PSI-MI-alternate [] synonym: "[R:po]" EXACT PSI-MI-alternate [] synonym: "alpha-amino-delta-phosphonoguanidinovaleric acid" EXACT PSI-MI-alternate [] synonym: "N5-[imino(phosphonoamino)methyl]-L-ornithine" EXACT PSI-MI-alternate [] synonym: "omega-N-phospho-L-arginine" EXACT PSI-MI-alternate [] synonym: "phosphoarginine" EXACT PSI-MI-short [] synonym: "RPO" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0172 name: aspartic 4-phosphoric anhydride def: "Residue modification.\nOBSOLETE remap to MOD:00042." [PMID:11125103, RESID:AA0033] synonym: "(S)-2-aminobutanedioic 4-phosphoric anhydride" EXACT PSI-MI-alternate [] synonym: "[D:po]" EXACT PSI-MI-alternate [] synonym: "beta-aspartyl phosphate" EXACT PSI-MI-alternate [] synonym: "DPO" EXACT PSI-MI-alternate [] synonym: "L-aspartic 4-phosphoric anhydride" EXACT PSI-MI-alternate [] synonym: "phosphoaspartic acid" EXACT PSI-MI-alternate [] synonym: "phosphoaspartic acid" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0173 name: s-phospho-cysteine def: "Residue modification.\nOBSOLETE remap to MOD:00043." [PMID:11125103, RESID:AA0034] synonym: "(R)-2-amino-3-(phosphonosulfanyl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "[C:po]" EXACT PSI-MI-alternate [] synonym: "CPO" EXACT PSI-MI-alternate [] synonym: "cysteine phosphate thioester" EXACT PSI-MI-alternate [] synonym: "phosphocysteine" EXACT PSI-MI-short [] synonym: "S-phospho-L-cysteine" EXACT PSI-MI-alternate [] synonym: "S-phosphonocysteine" EXACT PSI-MI-alternate [] synonym: "S3-phosphocysteine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0176 name: o-phospho-serine def: "Residue modification.\nOBSOLETE remap to MOD:00046." [PMID:11125103, RESID:AA0037] synonym: "(S)-2-amino-3-(phosphonooxy)propanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-3-hydroxypropanoic acid 3-phosphate" EXACT PSI-MI-alternate [] synonym: "2-amino-3-hydroxypropanoic acid 3-phosphate;O-phosphonoserine;O3-phosphoserine" EXACT PSI-MI-alternate [] synonym: "[S:po]" EXACT PSI-MI-alternate [] synonym: "O-phospho-L-serine" EXACT PSI-MI-alternate [] synonym: "O-phosphonoserine" EXACT PSI-MI-alternate [] synonym: "O3-phosphoserine" EXACT PSI-MI-alternate [] synonym: "phosphoserine" EXACT PSI-MI-short [] synonym: "serine phosphate ester" EXACT PSI-MI-alternate [] synonym: "SPO" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0177 name: o-phospho-threonine def: "Residue modification.\nOBSOLETE remap to MOD:00047." [PMID:11125103, RESID:AA0038] synonym: "(2S,3R)-2-amino-3-phosphonooxybutanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-3-hydroxybutanoic acid 3-phosphate" EXACT PSI-MI-alternate [] synonym: "[T:po]" EXACT PSI-MI-alternate [] synonym: "O-phospho-L-threonine" EXACT PSI-MI-alternate [] synonym: "O3-phosphothreonine" EXACT PSI-MI-alternate [] synonym: "phosphothreonine" EXACT PSI-MI-short [] synonym: "threonine phosphate ester" EXACT PSI-MI-alternate [] synonym: "TPO" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0178 name: o4'-phospho-tyrosine def: "Residue modification.\nOBSOLETE remap to MOD:00048." [PMID:11125103, RESID:AA0039] synonym: "(S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate" EXACT PSI-MI-alternate [] synonym: "[Y:po]" EXACT PSI-MI-alternate [] synonym: "O4'-phospho-L-tyrosine" EXACT PSI-MI-alternate [] synonym: "O4-phosphotyrosine" EXACT PSI-MI-alternate [] synonym: "phosphotyrosine" EXACT PSI-MI-short [] synonym: "tyrosine phosphate" EXACT PSI-MI-alternate [] synonym: "YPO" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0179 name: other modification def: "Residue modification.\nOBSOLETE remap to MOD:00032." [PMID:11125103] is_obsolete: true [Term] id: MI:0180 name: selenocysteine def: "Residue modification.\nOBSOLETE remap to MOD:00031." [PMID:11125103, RESID:AA0022] synonym: "3-selenylalanine" EXACT PSI-MI-alternate [] synonym: "[C:sel]" EXACT PSI-MI-alternate [] synonym: "CSE" EXACT PSI-MI-alternate [] synonym: "L-selenocysteine" EXACT PSI-MI-alternate [] synonym: "selenium cysteine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0181 name: selenomethionine def: "Residue modification.\nOBSOLETE remap to MOD:00530." [PMID:11125103] synonym: "[M:sel]" EXACT PSI-MI-alternate [] synonym: "L-selenomethionine" EXACT PSI-MI-alternate [] synonym: "MSE" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0182 name: 3-oxoalanine def: "Residue modification.\nOBSOLETE remap to MOD:01169." [PMID:11125103, RESID:AA0185] synonym: "(S)-2-amino-3-oxopropanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-3-oxopropionic acid" EXACT PSI-MI-alternate [] synonym: "[S:oxal]" EXACT PSI-MI-alternate [] synonym: "L-3-oxoalanine" EXACT PSI-MI-alternate [] synonym: "L-alpha-formylglycine" EXACT PSI-MI-alternate [] synonym: "L-amino-malonic acid semialdehyde" EXACT PSI-MI-alternate [] synonym: "L-aminomalonaldehydic acid" EXACT PSI-MI-alternate [] synonym: "L-serinesemialdehyde [misnomer]" EXACT PSI-MI-alternate [] synonym: "oxoalanine" EXACT PSI-MI-short [] synonym: "SOX" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0184 name: glutamyl 5-glycerylphosphorylethanolamine def: "Residue modification.\nOBSOLETE remap to MOD:00179." [PMID:11125103, RESID:AA0170] synonym: "(S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid" EXACT PSI-MI-alternate [] synonym: "[E:gpe]" EXACT PSI-MI-alternate [] synonym: "EGE" EXACT PSI-MI-alternate [] synonym: "glycerylpo4etohamine" EXACT PSI-MI-short [] synonym: "L-glutamyl 5-glycerophosphoethanolamine" EXACT PSI-MI-alternate [] synonym: "L-glutamyl 5-glycerophosphorylethanolamine" EXACT PSI-MI-alternate [] synonym: "L-glutamyl 5-glycerylphosphorylethanolamine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0186 name: n6-biotinyl-lysine def: "Residue modification.\nOBSOLETE remap to MOD:00126." [PMID:11125103, RESID:AA0117] synonym: "(3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine" EXACT PSI-MI-alternate [] synonym: "(S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid" EXACT PSI-MI-alternate [] synonym: "[K:biotin]" EXACT PSI-MI-alternate [] synonym: "biocytin" EXACT PSI-MI-alternate [] synonym: "biotinyllysine" EXACT PSI-MI-short [] synonym: "epsilon-N-biotinyllysine" EXACT PSI-MI-alternate [] synonym: "KBT" EXACT PSI-MI-alternate [] synonym: "N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine" EXACT PSI-MI-alternate [] synonym: "N6-biotinyl-L-lysine" EXACT PSI-MI-alternate [] synonym: "N6-biotinyllysine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0187 name: n6-(4-amino-2-hydroxybutyl)-lysine def: "Residue modification.\nOBSOLETE remap to MOD:00125." [PMID:11125103, RESID:AA0116] synonym: "(S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid" EXACT PSI-MI-alternate [] synonym: "[K:hypu]" EXACT PSI-MI-alternate [] synonym: "hypusine" EXACT PSI-MI-alternate [] synonym: "hypusine" EXACT PSI-MI-short [] synonym: "KHY" EXACT PSI-MI-alternate [] synonym: "N6-(4-amino-2-hydroxybutyl)-L-lysine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0188 name: n6-retinal-lysine def: "Residue modification.\nOBSOLETE remap to MOD:00129." [PMID:11125103, RESID:AA0120] synonym: "(S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid" EXACT PSI-MI-alternate [] synonym: "[K:retin]" EXACT PSI-MI-alternate [] synonym: "KRT" EXACT PSI-MI-alternate [] synonym: "N6-retinal-L-lysine" EXACT PSI-MI-alternate [] synonym: "N6-retinyl-lysine" EXACT PSI-MI-alternate [] synonym: "N6-retinylidene-L-lysine" EXACT PSI-MI-alternate [] synonym: "retinallysine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0189 name: ubiquitinated lysine def: "Residue modification due to a cross-link between a lysine and a glycine from the ubiquitine protein.\nOBSOLETE remap to MOD:00134." [PMID:11125103, RESID:AA0125] synonym: "[K:ub]" EXACT PSI-MI-alternate [] synonym: "KUB" EXACT PSI-MI-alternate [] synonym: "N6-glycyl-L-lysine" EXACT PSI-MI-alternate [] synonym: "N6-glycyllysine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0190 name: interaction type def: "Connection between molecule." [PMID:14755292] subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0191 name: aggregation def: "Physical association among molecules.\nOBSOLETE since too non-specific. Consider using physical interaction (MI:0218) instead." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0192 name: acetylation reaction def: "Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues." [GO:0006473, PMID:14755292, RESID:AA0041, RESID:AA0042, RESID:AA0043, RESID:AA0044, RESID:AA0045, RESID:AA0046, RESID:AA0047, RESID:AA0048, RESID:AA0049, RESID:AA0050, RESID:AA0051, RESID:AA0052, RESID:AA0053, RESID:AA0054, RESID:AA0055, RESID:AA0056] subset: PSI-MI_slim synonym: "acetylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0193 name: amidation reaction def: "Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues. It involves the addition of an amide group from a glycine to the target residue." [GO:0001519, PMID:14755292, RESID:AA0081, RESID:AA0082, RESID:AA0083, RESID:AA0084, RESID:AA0085, RESID:AA0086, RESID:AA0087, RESID:AA0088, RESID:AA0089, RESID:AA0090, RESID:AA0091, RESID:AA0092, RESID:AA0093, RESID:AA0094, RESID:AA0095, RESID:AA0096, RESID:AA0097, RESID:AA0098, RESID:AA0099, RESID:AA0100] subset: PSI-MI_slim synonym: "amidation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0194 name: cleavage reaction def: "Covalent bond breakage in a molecule leading to the formation of smaller molecules." [PMID:14755292] subset: PSI-MI_slim synonym: "cleavage" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0195 name: covalent binding def: "Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0407 ! direct interaction [Term] id: MI:0196 name: covalent interaction def: "Physical interaction mediated by covalent bond rearrangement.\nOBSOLETE use covalent binding (MI:0195) instead." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0197 name: deacetylation reaction def: "N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues." [GO:0006476, PMID:14755292, RESID:AA0055, RESID:AA0056] subset: PSI-MI_slim synonym: "deacetylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0198 name: defarnesylation reaction def: "S-farnesyl-L-cysteined is cleaved and returns a C residue." [PMID:14755292, RESID:AA0102] subset: PSI-MI_slim synonym: "defarnesylation" EXACT PSI-MI-short [] is_a: MI:0212 ! lipoprotein cleavage reaction [Term] id: MI:0199 name: deformylation reaction def: "N6-formyl-L-lysine is cleaved and returns a K residue." [PMID:14755292, RESID:AA0211] subset: PSI-MI_slim synonym: "deformylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0200 name: degeranylation reaction def: "S-geranylgeranyl-L-cysteine is cleaved and returns a C residue." [PMID:14755292, RESID:AA0104] subset: PSI-MI_slim synonym: "degeranylation" EXACT PSI-MI-short [] is_a: MI:0212 ! lipoprotein cleavage reaction [Term] id: MI:0201 name: demyristoylation reaction def: "N6-myristoyl-L-lysine is cleaved and returns a K residue." [PMID:14755292, RESID:AA0078] subset: PSI-MI_slim synonym: "demyristoylation" EXACT PSI-MI-short [] is_a: MI:0212 ! lipoprotein cleavage reaction [Term] id: MI:0202 name: depalmitoylation reaction def: "S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues." [PMID:14755292, RESID:AA0060, RESID:AA0077, RESID:AA0106] subset: PSI-MI_slim synonym: "depalmitoylation" EXACT PSI-MI-short [] is_a: MI:0212 ! lipoprotein cleavage reaction [Term] id: MI:0203 name: dephosphorylation reaction def: "Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues." [GO:0016311, PMID:14755292, RESID:AA0033, RESID:AA0034, RESID:AA0035, RESID:AA0036, RESID:AA0037, RESID:AA0038, RESID:AA0039, RESID:AA0222] subset: PSI-MI_slim synonym: "dephosphorylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0204 name: deubiquitination reaction def: "Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins." [GO:0016579, PMID:11583613, RESID:AA0125] subset: PSI-MI_slim synonym: "deubiquitination" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0205 name: disaggregation def: "Dissociation of partners interacting via non-covalent bond.\nOBSOLETE because considered misleading." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0206 name: farnesylation reaction def: "Reversible reaction that can affect C residue." [GO:0018347, PMID:14755292, RESID:AA0102] subset: PSI-MI_slim synonym: "farnesylation" EXACT PSI-MI-short [] is_a: MI:0211 ! lipid addition [Term] id: MI:0207 name: formylation reaction def: "Reaction that can affect K or G residues. Reside is functionalised with a formyl group." [GO:0018256, PMID:14755292, RESID:AA0057, RESID:AA0211] subset: PSI-MI_slim synonym: "formylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0208 name: genetic interaction def: "An effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations.\nab (not=) E" [PMID:16527956] subset: PSI-MI_slim is_a: MI:0190 ! interaction type [Term] id: MI:0209 name: geranylgeranylation reaction def: "Attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).Reversible reaction that can affect C residue." [GO:0018348, PMID:14755292, RESID:AA0104] subset: PSI-MI_slim synonym: "geranylgeranylation" EXACT PSI-MI-short [] is_a: MI:0211 ! lipid addition [Term] id: MI:0210 name: hydroxylation reaction def: "Irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. Hydroxylation is the first step in the oxidative degeneration of organic compounds." [GO:0018126, PMID:14755292, RESID:AA0028, RESID:AA0029, RESID:AA0030, RESID:AA0146, RESID:AA0215] subset: PSI-MI_slim synonym: "hydroxylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0211 name: lipid addition def: "Covalent or non covalent binding of lipid group on a protein residue." [GO:0006497, PMID:14755292] subset: PSI-MI_slim is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0212 name: lipoprotein cleavage reaction def: "Cleavage of a lipid group covalently bound to a protein residue." [PMID:14755292] subset: PSI-MI_slim synonym: "lipid cleavage" EXACT PSI-MI-short [] is_a: MI:0194 ! cleavage reaction [Term] id: MI:0213 name: methylation reaction def: "The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues." [GO:0043414, PMID:14755292, RESID:AA0061, RESID:AA0062, RESID:AA0063, RESID:AA0064, RESID:AA0065, RESID:AA0066, RESID:AA0067, RESID:AA0068, RESID:AA0069, RESID:AA0070, RESID:AA0071, RESID:AA0072, RESID:AA0073, RESID:AA0074, RESID:AA0075, RESID:AA0076, RESID:AA0234, RESID:AA0272] subset: PSI-MI_slim synonym: "methylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0214 name: myristoylation reaction def: "Irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. Reaction that can affect K or G residues." [GO:0018319, PMID:14755292, RESID:AA0059, RESID:AA0078] subset: PSI-MI_slim synonym: "myristoylation" EXACT PSI-MI-short [] is_a: MI:0211 ! lipid addition [Term] id: MI:0215 name: non covalent interaction def: "Interaction mediated by non-covalent, weak forces rearrangement.\nOBSOLETE use physical interaction (MI:0218) instead." [PMID:14755292] subset: PSI-MI_slim synonym: "non covalent inter" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0216 name: palmitoylation reaction def: "Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues." [GO:0018318, PMID:14755292, RESID:AA0060, RESID:AA0077, RESID:AA0079, RESID:AA0080, RESID:AA0106] subset: PSI-MI_slim synonym: "palmitoylation" EXACT PSI-MI-short [] is_a: MI:0211 ! lipid addition [Term] id: MI:0217 name: phosphorylation reaction def: "Reversible reaction that can affect D,C,H,S,T,Y,R residues." [GO:0016310, PMID:14755292, RESID:AA0033, RESID:AA0034, RESID:AA0035, RESID:AA0036, RESID:AA0037, RESID:AA0038, RESID:AA0039, RESID:AA0222] subset: PSI-MI_slim synonym: "phosphorylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0218 name: physical interaction def: "Interaction among molecules that can be direct or indirect.\nOBSOLETE: splitted to 'association' MI:0914 and 'physical association' MI:0915. For remapping consider the experimental setting of an interaction. For bulk remapping a possible criteria is to whatever physical interaction that has among its participant a bait should become 'association' MI:0914 the others can become 'physical association' MI:0915. Two hybrid interactions are an expection and can be 'physical association' MI:0915." [PMID:14755292] is_obsolete: true [Term] id: MI:0219 name: synthetic lethal def: "Death phenotype observed on cells carrying combination of two independently silent mutations.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)" [PMID:15608217] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0220 name: ubiquitination reaction def: "Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target." [GO:0016567, PMID:11583613, RESID:AA0125] subset: PSI-MI_slim synonym: "ubiquitination" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0221 name: expression level def: "Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0346 ! experimental preparation [Term] id: MI:0222 name: physiological level def: "A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate." [PMID:14755292] subset: PSI-MI_slim synonym: "endogenous" EXACT PSI-MI-alternate [] synonym: "endogenous level" EXACT PSI-MI-alternate [] is_a: MI:0221 ! expression level [Term] id: MI:0223 name: under expressed level def: "A molecule is estimated to be expressed at lower levels than in physiological condition." [PMID:14755292] subset: PSI-MI_slim synonym: "under-expressed" EXACT PSI-MI-short [] is_a: MI:0221 ! expression level is_a: MI:0803 ! expression level alteration [Term] id: MI:0225 name: chromatin immunoprecipitation array def: "The method combines a modified chromatin immunoprecipitation (ChIP) procedure, with DNA microarray analysis. Cells are fixed with formaldehyde, harvested, and disrupted by sonication. The DNA fragments cross-linked to a protein of interest are enriched by immunoprecipitation with a specific antibody. After reversal of the cross-links, the enriched DNA is amplified and labeled with a fluorescent dye (Cy5) by using a ligation-mediatedpolymerase chain reaction (LM-PCR). In parallel a sample of DNA that is not enriched by immunoprecipitation is subjected to LM-PCR in the presence of a different fluorophore (Cy3), and both immunoprecipitation (IP)-enriched and unenriched pools of labeled DNA were hybridized to a single DNA microarray containing a set of intergenic sequences. The ratio of the Cy5 to Cy3 fluorescence intensities measured at each DNA element in the microarray provided a measure of the extent of binding of the transcription factor to the corresponding genomic locus." [PMID:11125145, PMID:11206552] subset: PSI-MI_slim synonym: "chip-chip" EXACT PSI-MI-short [] is_a: MI:0008 ! array technology is_a: MI:0402 ! chromatin immunoprecipitation assay [Term] id: MI:0226 name: ion exchange chromatography def: "Stable complexes and their component proteins can be separated on the basis of their net charge by ion-exchange chromatography. If a protein has a net positive charge at pH 7, it will usually bind to a column of beads containing carboxylate groups, and can then be eluted by increasing the concentration of sodium chloride or another salt in the eluting buffer by competition of sodium ions with positively charged groups on the protein for binding to the column. Protein that have a low density of net positive charge will tend to emerge first, followed by those having a higher charge density. Positively charged complexes or proteins (cationic proteins) can be separated on negatively charged carboxymethyl-cellulose (CM-cellulose) columns. Conversely, negatively charged complexes or proteins (anionic proteins) can be separated by chromatography on positively charged diethylaminoethyl-cellulose (DEAE-cellulose) columns." [PMID:14755292] subset: PSI-MI_slim synonym: "IEC" EXACT PSI-MI-alternate [] synonym: "ion exchange chrom" EXACT PSI-MI-short [] is_a: MI:0091 ! chromatography technology [Term] id: MI:0227 name: reverse phase chromatography def: "Reverse phase chromatography operates on the basis of hydrophilicity and lipophilicity. The stationary phase consists of silica based packings with n-alkyl chains covalently bound. For example, C-8 signifies an octyl chain and C-18 an octadecyl ligand in the matrix. The more hydrophobic the matrix on each ligand, the greater is the tendency of the column to retain hydrophobic moieties. Thus hydrophilic compounds elute more quickly than do hydrophobic compounds." [PMID:14755292] subset: PSI-MI_slim synonym: "reverse phase chrom" EXACT PSI-MI-short [] is_a: MI:0091 ! chromatography technology [Term] id: MI:0228 name: cytoplasmic complementation assay def: "Protein complementation assay performed by dissecting a cytoplasmic protein activity and restoring it through the two hybrid proteins interaction. OBSOLETE remap to MI:0090 protein complementation assay" [PMID:14755292] subset: PSI-MI_slim synonym: "cytoplasmic compl" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0230 name: membrane bound complementation assay def: "OBSOLETE remap to MI:0090 protein complementation assay." [PMID:14755292] subset: PSI-MI_slim synonym: "membrane compl" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0231 name: mammalian protein protein interaction trap def: "The MAPPIT(mammalian protein-protein interaction Trap) is a screening method for protein-protein interaction in mammalian cells, based on the reconstitution of a membrane STAT (signal transducers and activators of transcription) receptor. The bait protein is fused to a STAT recruitment-deficient receptor and the prey protein to a functional STAT recruitment sites. In such a configuration, a given baitprey interaction restores a STAT-dependent responses leading to the expression of a reporter gene. This system, enable to demonstrate not only protein interaction but also modification-independent and tyrosine phosphorylation- dependent interactions." [PMID:12853652] subset: PSI-MI_slim synonym: "mappit" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0232 name: transcriptional complementation assay def: "Protein complementation assay performed by dissecting a transcription factor activity (DNA binding domain and transcription activation domain) its restoration through the two hybrid proteins interaction that lead to a reporter gene expression." [PMID:14755292] subset: PSI-MI_slim synonym: "transcription compl" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0233 name: protein dna complex def: "A stable set of interacting protein and DNA that can be copurified and operate as a functional unit." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1299 ! complex composition [Term] id: MI:0234 name: 131i radiolabel def: "Molecule labelled with 131 radio isotope of iodine atoms." [PMID:14755292] subset: PSI-MI_slim synonym: "131I" EXACT PSI-MI-alternate [] synonym: "I131" EXACT PSI-MI-alternate [] is_a: MI:0517 ! radiolabel [Term] id: MI:0235 name: 14c radiolabel def: "Molecule labelled with the radio isotope 14 of carbon atoms." [PMID:14755292] subset: PSI-MI_slim synonym: "14C" EXACT PSI-MI-alternate [] synonym: "C14" EXACT PSI-MI-alternate [] is_a: MI:0517 ! radiolabel [Term] id: MI:0236 name: 32p radiolabel def: "Molecule labelled with the radio isotope 32 of phosphorus atoms." [PMID:14755292] subset: PSI-MI_slim synonym: "32P" EXACT PSI-MI-alternate [] synonym: "P32" EXACT PSI-MI-alternate [] is_a: MI:0517 ! radiolabel [Term] id: MI:0237 name: 33p radiolabel def: "Molecule labelled with the radio isotope 33 of phosphorus atoms." [PMID:14755292] subset: PSI-MI_slim synonym: "33P" EXACT PSI-MI-alternate [] synonym: "P33" EXACT PSI-MI-alternate [] is_a: MI:0517 ! radiolabel [Term] id: MI:0238 name: 3h radiolabel def: "Molecules labelled with isotope 3 of hydrogen atoms." [PMID:14755292] subset: PSI-MI_slim synonym: "3H" EXACT PSI-MI-alternate [] synonym: "H3" EXACT PSI-MI-alternate [] synonym: "tritium" EXACT PSI-MI-alternate [] is_a: MI:0517 ! radiolabel [Term] id: MI:0239 name: biotin tag def: "Biotin, a 244 Dalton vitamin found in tissue and blood, binds with high affinity to avidin and streptavidin protein. Since biotin is a relatively small molecule, it can be conjugated to many proteins or nucleic acids without significantly altering their biological activity. Biotinylation reagents are available for targeting a variety of specific functional groups, including primary amines, sulfhydryls, carboxyls and carbohydrates that lead to nucleotides or amino acid biotinilation." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0507 ! tag [Term] id: MI:0240 name: fusion protein def: "The protein under study is expressed as a fusion with a labelling protein, having either fluorescence properties or an enzymatic activity that facilitates its purification, identification, localisation or quantification." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0507 ! tag [Term] id: MI:0241 name: horseradish peroxidase tag def: "Protein is fused to horseradish peroxidase, and the measure of this enzyme activity can be taken as indicative of presence of protein." [PMID:14755292] subset: PSI-MI_slim synonym: "hrp tag" EXACT PSI-MI-short [] is_a: MI:0365 ! enzyme tag [Term] id: MI:0242 name: gene ontology definition reference def: "This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference." [PMID:14755292] subset: PSI-MI_slim synonym: "go-definition-ref" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0243 name: isoform parent sequence reference def: "Reference to the master sequence from which this isoform has been derived." [PMID:14755292] subset: PSI-MI_slim synonym: "isoform-parent" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0244 name: reactome complex def: "Collection of functional complexes within Reactome - a knowledgebase of biological processes.\nhttp://www.reactome.org/. OSOLETE - this concept no longer exists within Reactome." [PMID:21067998] subset: PSI-MI_slim xref: id-validation-regexp: "REACT_[0-9]{1,5}\\.[0-9]{1,3}|[0-9]+" xref: search-url: "http://www.reactome.org/cgi-bin/eventbrowser?ID=${ac}" is_obsolete: true [Term] id: MI:0245 name: reactome protein def: "Collection of protein within the Reactome database - a knowledgebase of biological processes.\nhttp://www.reactome.org/. OBSOLETE - this concept no longer exists within Reactome." [PMID:21067998] subset: PSI-MI_slim xref: id-validation-regexp: "REACT_[0-9]{1,4}\\.[0-9]{1,3}|[OPQ][0-9][A-Z0-9]{3}[0-9]|[OPQ][0-9][A-Z0-9]{3}[0-9]-[0-9]+|[A-Z]{3}[0-9]{5}|[OPQ][0-9][A-Z0-9]{3}[0-9]-PRO_[0-9]{10}" xref: search-url: "http://www.reactome.org/cgi-bin/link?SOURCE=UNIPROT&ID=${ac}" is_obsolete: true [Term] id: MI:0246 name: cabri def: "CABRI cell lines catalogue available at.\nhttp://www.cabri.org/" [PMID:14755292] subset: PSI-MI_slim xref: id-validation-regexp: "[0-9]+|ACC\\s[A-Z0-9]+|ECACC\\s[A-Z0-9]+|LMBP\\s[A-Z0-9]+|ICLC\\s[A-Z0-9]+|CIP-[0-9]+|DSMZ_MUTZ\\:ACC\\s[0-9]+" xref: search-url: "http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$id]" is_a: MI:0473 ! participant database [Term] id: MI:0247 name: newt def: "New EBI Web Taxonomy.\nhttp://www.ebi.ac.uk/newt OBSOLETE: Consider remapping to uniprot taxonomy MI:0942" [PMID:14755292] subset: PSI-MI_slim xref: id-validation-regexp: "[0-9]+" xref: search-url: "http://www.ebi.ac.uk/newt/display?search=${ac}" is_obsolete: true [Term] id: MI:0248 name: resid def: "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.\nhttp://www.ebi.ac.uk/RESID/index.html" [PMID:14755292] subset: PSI-MI_slim xref: id-validation-regexp: "AA[0-9]{4}" xref: search-url: "http://srs.ebi.ac.uk/cgi-bin/wgetz?[resid-id:${ac}]+-e" is_a: MI:0447 ! feature database [Term] id: MI:0249 name: huge def: "A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project.\nhttp://www.kazusa.or.jp/huge/" [PMID:14755292] subset: PSI-MI_slim xref: id-validation-regexp: "KIAA[0-9]{4}[A-Z]{0,1}" xref: search-url: "http://www.kazusa.or.jp/huge/gfpage/${ac}" is_a: MI:0683 ! sequence database [Term] id: MI:0250 name: gene def: "interactor for genetic interaction." [PMID:14755292, SO:0000704] subset: PSI-MI_slim is_a: MI:0313 ! interactor type [Term] id: MI:0251 name: gene product def: "Reference of a protein object pointing to its genomic or nucleic acid sequence." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0252 name: biological feature def: "Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0116 ! feature type [Term] id: MI:0253 name: isotope label def: "One of several nuclides having the same number of protons in their nuclei and hence having the same atomic number, but differing in the number of neutrons and therefore, in the mass number." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0505 ! experimental feature [Term] id: MI:0254 name: genetic interference def: "This term refers to methods that aim at interfering with the activity of a specific gene by altering the gene regulatory or coding sequences. This goal can be achieved either by a classical genetic approach (random mutagenesis followed by phenotype characterization and genetic mapping) or by a reverse genetics approach where a gene of interest is modified by directed mutagenesis." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0045 ! experimental interaction detection [Term] id: MI:0255 name: post transcriptional interference def: "This term refers to methods designed to interfere with gene expression at post-transcriptional level rather than with the gene itself." [PMID:14755292] subset: PSI-MI_slim synonym: "expression interfer" EXACT PSI-MI-short [] is_a: MI:0045 ! experimental interaction detection [Term] id: MI:0256 name: rna interference def: "RNA interference (RNAi) is a post-transcriptional gene silencing method reproducing a naturally occurring phenomena. RNAi is the process whereby double-stranded RNA (dsRNA) induces the sequence-specific degradation of homologous mRNA. RNAi or dsRNA-induced silencing phenomena are present in evolutionarily diverse organisms, e.g., nematodes, plants, fungi, and trypanosomes. The mechanisms by which RNAi works is initiated by a progressive cleavage of dsRNA into 21 to 23 nucleotide (nt) short interfering RNAs (siRNAs). These native siRNA duplexes are then incorporated into a protein complex called RNA-induced silencing complex (RISC). ATP-dependent unwinding of the siRNA duplex generates an active RISC complex. Guided by the antisense strand of siRNA, the active RISC complex recognizes and cleaves the corresponding mRNA." [PMID:12110901, PMID:12408823] subset: PSI-MI_slim synonym: "rnai" EXACT PSI-MI-short [] is_a: MI:0255 ! post transcriptional interference [Term] id: MI:0257 name: antisense rna def: "This approach is based on the observation that expression of RNA that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation." [PMID:1340158] subset: PSI-MI_slim is_a: MI:0255 ! post transcriptional interference [Term] id: MI:0258 name: inhibitor antibodies def: "Intracellular or extracellular expression of antibodies is used to target specific gene products in order to inactivate them. Most of the times the antibody scaffold need s to reengineered for efficient expression and solubility in the cytoplasm.\nOBSOLETE as such method can be described using the biological role inhibitor (MI:0586)." [PMID:10189716] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0259 name: perturbagens peptides def: "This approach is based on the expression of peptides that bind to specific target proteins thereby interfering with their activity. In a standard approach the interfering peptide is expressed by genetic fusion to a stable protein scaffold. Interfering peptides can also be introduced into cells by fusing them to proteins or peptides (homeodomains, Tat protein.) having the property of penetrating the cell membrane. The peptide-carrier fusion protein is either synthesized chemically or produced in vivo, normally in bacteria. When the purified fusion protein is added to a cell culture, it penetrates the cell membrane thereby permitting the fused peptide to interfere with its target protein.\nOBSOLETE as such method can be described using the biological role inhibitor (MI:0586)." [PMID:11731788, PMID:8606778] subset: PSI-MI_slim synonym: "perturbagens pep" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0260 name: inhibitor small molecules def: "Protein activity is inhibited by small inorganic molecules (drugs) that specifically bind to their targets. Recently this classical pharmacological approach is sometime referred to as 'chemical genetics'.\nOBSOLETE as such method can be described using the biological role inhibitor (MI:0586)." [PMID:10542155, PMID:10780927] subset: PSI-MI_slim synonym: "inhibitor small mol" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0261 name: suppression def: "A supressed gene mutation cause of an altered phenotype that is reverted to wild type phenotype when cell also carry a suppressor gene with a specific mutation or altered expression level.\nOBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793." [PMID:15608217] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0262 name: suppression mutation def: "A given (suppressed) mutation phenotype is reverted by a supressor gene mutation.\nOBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'mutated gene' MI:0804. " [PMID:15608217] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0263 name: suppression knockout def: "Knocked out gene is the suppressor of a phenotype.\nOBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock out' MI:0788. " [PMID:15608217] subset: PSI-MI_slim synonym: "suppress knockout" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0264 name: suppression partial alteration def: "A mutation is the partial suppressor of a mutant phenotype.\nOBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock down' MI:0789. " [PMID:15608217] subset: PSI-MI_slim synonym: "suppression partial" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0265 name: suppression expression alteration def: "An altered expression is the suppressor of a phenotype.\nOBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803. " [PMID:15608217] subset: PSI-MI_slim synonym: "suppress expression" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0266 name: suppression overexpression def: "Overexpression is the suppressor of a phenotype.\nOBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'over expressed' MI:0506. " [PMID:15608217] subset: PSI-MI_slim synonym: "suppress overexpress" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0267 name: suppression scalable def: "Level of over/underexpression scales the 'extend' of a phenotype.\nOBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803. " [PMID:15608217] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0268 name: suppression underexpression def: "Underexpression is the suppressor of a phenotype.\nOBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'under expressed' MI:0223. " [PMID:15608217] subset: PSI-MI_slim synonym: "suppress underexpres" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0269 name: synthetic phenotype def: "Two silent mutations show an altered phenotype when they co-occur on the same cell.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794." [PMID:15608217] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0270 name: conditional synthetic lethal def: "Two silent mutations show a conditional synthetic lethal phenotype when they co-occur on the same cell.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)" [PMID:15608217] subset: PSI-MI_slim synonym: "cond syntetic lethal" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0271 name: conditional synthetic lethal temperature-sensitivity def: "Two silent mutations show a temperature sensitive lethal phenotype when they co-occur on the same cell.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (FBcv:0000310 'temperature conditional')" [PMID:15608217] subset: PSI-MI_slim synonym: "temprtr synt lethal" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0273 name: synthetic growth effect def: "Two silent mutations show altered growth effect when they co-occur on the same cell.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')" [PMID:15608217] subset: PSI-MI_slim synonym: "synt growth effect" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0274 name: synthetic growth defect def: "Two silent mutations show growth defect when they co-occur on the same cell.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')" [PMID:15608217] subset: PSI-MI_slim synonym: "synt growth defect" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0275 name: synthetic growth increase def: "Two silent mutations show growth increase when they co-occur on the same cell.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')" [PMID:15608217] subset: PSI-MI_slim synonym: "synt growth increase" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0276 name: blue native page def: "Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. Blue native (BN)-PAGE is a charge shift method, in which the electrophoretic mobility of a complex is determined by the negative charge of the bound Coomassie dye and the size and shape of the complex. Coomassie does not act as a detergent and preserves the structure of complexes. Importantly, the resolution of BN-PAGE is much higher than that of other methods such as gel filtration or sucrose-gradient ultracentrifugation. Combined with other pre-purifications or dialysis steps this method permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE." [PMID:14665681] subset: PSI-MI_slim synonym: "bn-page" EXACT PSI-MI-short [] is_a: MI:0404 ! comigration in non denaturing gel electrophoresis [Term] id: MI:0300 name: alias type def: "Descriptor of type of nomenclature used to describe interactor." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "CvAliasType" EXACT PSI-MI-alternate [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0301 name: gene name def: "Gene name." [PMID:14755292] subset: PSI-MI_slim synonym: "gene" EXACT PSI-MI-alternate [] is_a: MI:1041 ! synonym [Term] id: MI:0302 name: gene name synonym def: "Gene name synonym." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1041 ! synonym [Term] id: MI:0303 name: gene ontology synonym def: "Synonym as used in Gene Ontology." [PMID:14755292] subset: PSI-MI_slim synonym: "go synonym" EXACT PSI-MI-short [] is_a: MI:1041 ! synonym [Term] id: MI:0304 name: isoform synonym def: "Isoform synonym." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1041 ! synonym [Term] id: MI:0305 name: ordered locus name def: "A name used to represent an ORF in a completely sequenced genome or chromosome. It is generally based on a prefix representing the organism and a number which usually represents the sequential ordering of genes on the chromosome. Depending on the genome sequencing center, numbers are attributed only to protein-coding genes, or also to pseudogenes, or also to tRNAs and other features." [PMID:14755292] comment: For instance HI0934, Rv3245c, At5g34500, YER456W. subset: PSI-MI_slim synonym: "CDS number" EXACT PSI-MI-alternate [] synonym: "locus name" EXACT PSI-MI-short [] synonym: "ONL" EXACT PSI-MI-alternate [] synonym: "Ordered locus name" EXACT PSI-MI-alternate [] synonym: "ORF number" EXACT PSI-MI-alternate [] synonym: "systematic gene number" EXACT PSI-MI-alternate [] is_a: MI:1041 ! synonym [Term] id: MI:0306 name: open reading frame name def: "A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system." [PMID:14755292] comment: For instance MtCY277-28c, SYGP-ORF50, SpBC2F12-04, C06E1, CG10954. Also called Sequencing names or Contig names or Temporary ORFNames. subset: PSI-MI_slim synonym: "orf name" EXACT PSI-MI-short [] is_a: MI:1041 ! synonym [Term] id: MI:0307 name: delivery method def: "Method by which molecule is delivered or engineered into a cell." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0346 ! experimental preparation [Term] id: MI:0308 name: electroporation def: "Method for temporarily permeabilising cell membranes so as to facilitate the entry of large or hydrophilic molecules (as in transfection). A brief (ca 1 msec) electric pulse is given with potential gradients of about 700V/cm." [PMID:6329708] subset: PSI-MI_slim is_a: MI:0307 ! delivery method [Term] id: MI:0309 name: genomic tagging def: "A cassette coding for a protein tag is inserted by homologous recombination onto the genomic copy of an open reading frame. The advantage of this delivery method is that the resulting engineered protein is expressed under its natural promoter control.\nOBSOLETE redundant term. Map to feature type : tag (MI:0507)." [PMID:14755292] subset: PSI-MI_slim synonym: "genetic tag insertion" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0310 name: infection def: "Molecule introduced into a cell via an external organism, usually a virus or bacteria." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0307 ! delivery method [Term] id: MI:0311 name: microinjection def: "The insertion of a substance into a cell through a microneedle. To extrude the substances through the very fine needle tip, either hydrostatic pressure (pressure injection) or electric currents (ionophoresis) is employed." [PMID:3016916] subset: PSI-MI_slim synonym: "micro-injection" EXACT PSI-MI-alternate [] is_a: MI:0307 ! delivery method [Term] id: MI:0312 name: nucleic acid transfection def: "Introducing DNA into eukaryotic cells, such as animal cells, is called transfection. Transfection typically involves opening transient \"holes\" or gates in cells to allow the entry of extracellular molecules, typically supercoiled plasmid DNA, but also siRNA, among others. Transfection differs from transformation since the DNA is not generally incorporated into the cell's genome, it is only transiently expressed." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl transfection" EXACT PSI-MI-short [] is_a: MI:0704 ! nucleic acid delivery [Term] id: MI:0313 name: interactor type def: "Molecular species involved in the interaction." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "participant type" EXACT PSI-MI-alternate [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0314 name: complex def: "Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0313 ! interactor type [Term] id: MI:0315 name: protein complex def: "A stable set of interacting proteins that can be copurified and operate as a functional unit." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1299 ! complex composition [Term] id: MI:0316 name: ribonucleoprotein complex def: "A macromolecular complex containing both protein and RNA molecules." [GO:0030529, PMID:14755292] subset: PSI-MI_slim synonym: "protein rna complex" EXACT PSI-MI-alternate [] synonym: "ribonucleoprot compl" EXACT PSI-MI-short [] is_a: MI:1299 ! complex composition [Term] id: MI:0317 name: interaction def: "Previously described interaction now being used as an interactor to describe hierarchical build-up of complexes." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0313 ! interactor type [Term] id: MI:0318 name: nucleic acid def: "Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages." [PMID:14755292, SO:0000348] subset: PSI-MI_slim is_a: MI:0383 ! biopolymer [Term] id: MI:0319 name: deoxyribonucleic acid def: "Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine." [PMID:14755292, SO:0000352] subset: PSI-MI_slim synonym: "deoxyribonucleic acid" EXACT PSI-MI-alternate [] synonym: "DNA" EXACT PSI-MI-alternate [] synonym: "dna" EXACT PSI-MI-short [] is_a: MI:0318 ! nucleic acid [Term] id: MI:0320 name: ribonucleic acid def: "Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine." [PMID:14755292, SO:0000356] subset: PSI-MI_slim synonym: "RNA" EXACT PSI-MI-alternate [] synonym: "rna" EXACT PSI-MI-short [] is_a: MI:0318 ! nucleic acid [Term] id: MI:0321 name: catalytic rna def: "Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link." [PMID:14755292] subset: PSI-MI_slim synonym: "catalytic ribonucleic acid" EXACT PSI-MI-alternate [] synonym: "catalytic RNA" EXACT PSI-MI-alternate [] synonym: "crna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0322 name: guide rna def: "Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing." [PMID:14755292] subset: PSI-MI_slim synonym: "grna" EXACT PSI-MI-short [] synonym: "guide RNA" EXACT PSI-MI-alternate [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0323 name: heterogeneous nuclear rna def: "A heterogeneous mixture of RNA molecules with a rapid turnover rate that occurs in cell nuclei during protein synthesis; it is the form of RNA synthesized in eukaryotes by RNA polymerase II, which is translated into protein." [PMID:14755292] subset: PSI-MI_slim synonym: "heterogeneous nuclear ribonucleic acid" EXACT PSI-MI-alternate [] synonym: "heterogeneous nuclear RNA" EXACT PSI-MI-alternate [] synonym: "hnrna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0324 name: messenger rna def: "Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains." [PMID:14755292] subset: PSI-MI_slim synonym: "mRNA" EXACT PSI-MI-alternate [] synonym: "mrna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0325 name: transfer rna def: "The low molecular weight RNAs that specifically bind amino acids by aminoacetylation to form aminoacyl tRNA and which possess a special nucleotide triplet, the anticodon." [PMID:14755292] subset: PSI-MI_slim synonym: "transfer ribonucleic acid" EXACT PSI-MI-alternate [] synonym: "transfer RNA" EXACT PSI-MI-alternate [] synonym: "tRNA" EXACT PSI-MI-alternate [] synonym: "trna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0326 name: protein def: "A linear polymer of amino acids joined by peptide bonds in a specific sequence." [PMID:14755292, SO:0000358] subset: PSI-MI_slim is_a: MI:0383 ! biopolymer [Term] id: MI:0327 name: peptide def: "Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues." [PMID:14755292] subset: PSI-MI_slim synonym: "oligopeptide" EXACT PSI-MI-alternate [] synonym: "polypeptide" EXACT PSI-MI-alternate [] is_a: MI:0383 ! biopolymer [Term] id: MI:0328 name: small molecule def: "Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity." [PMID:14755292] subset: Drugable subset: PSI-MI_slim is_a: MI:1100 ! bioactive entity [Term] id: MI:0329 name: unknown participant def: "Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0313 ! interactor type [Term] id: MI:0330 name: molecular source def: "Defines whether molecule is endogenously expressed or has in any way been altered, in sequence or expression level, from its native state. For a complete description of the experimental molecule form use the orthogonal CVs expression level, delivery method, and sample process." [PMID:14755272] subset: PSI-MI_slim is_a: MI:0346 ! experimental preparation [Term] id: MI:0331 name: engineered def: "Molecule has been added into system from an external source or altered within the cell." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0330 ! molecular source [Term] id: MI:0332 name: naturally occurring def: "Unaltered endogenous molecule in its naturally occurring state." [PMID:14755292] subset: PSI-MI_slim synonym: "endogenous" EXACT PSI-MI-alternate [] is_a: MI:0330 ! molecular source [Term] id: MI:0333 name: feature range status def: "Describes sequence positions resolution of a given participant feature. In PSI schema this CV is associated with the start and end position of a feature range." [PMID:14755292] subset: PSI-MI_slim synonym: "CvFuzzyType" EXACT PSI-MI-alternate [] synonym: "endStatus" EXACT PSI-MI-alternate [] synonym: "startStatus" EXACT PSI-MI-alternate [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0334 name: c-terminal position def: "Term describing the last amino acid of a peptide chain." [PMID:14755292] comment: Displayed as 'c'. subset: PSI-MI_slim synonym: "c-term" EXACT PSI-MI-alternate [] synonym: "c-terminal" EXACT PSI-MI-short [] synonym: "c-terminus" EXACT PSI-MI-alternate [] synonym: "carboxy-terminus" EXACT PSI-MI-alternate [] is_a: MI:0333 ! feature range status [Term] id: MI:0335 name: certain sequence position def: "Position within the sequence clearly defined." [PMID:14755292] subset: PSI-MI_slim synonym: "certain" EXACT PSI-MI-short [] is_a: MI:0333 ! feature range status [Term] id: MI:0336 name: greater-than def: "Partially determined sequence position known to be in a location higher than a given position." [PMID:14755292] comment: Displayed as '>'. subset: PSI-MI_slim is_a: MI:0333 ! feature range status [Term] id: MI:0337 name: less-than def: "Partially determined sequence position known to be in a position lower than a given position." [PMID:14755292] comment: Displayed as '<'. subset: PSI-MI_slim is_a: MI:0333 ! feature range status [Term] id: MI:0338 name: range def: "Describes a sequence position known to be in a certain range, where the exact position is unclear." [PMID:14755292] comment: For instance when an amino acid modification is known to be in the region from 5 to 7. Displayed as '..'. subset: PSI-MI_slim is_a: MI:0333 ! feature range status [Term] id: MI:0339 name: undetermined sequence position def: "Term describing a completely unknown or unspecified sequence position." [PMID:14755292] comment: Displayed as '?'. subset: PSI-MI_slim synonym: "undetermined" EXACT PSI-MI-short [] is_a: MI:0333 ! feature range status [Term] id: MI:0340 name: n-terminal position def: "Term describing the first amino acid of a peptide chain." [PMID:14755292] comment: Displayed as 'n'. subset: PSI-MI_slim synonym: "amino-terminus" EXACT PSI-MI-alternate [] synonym: "n-term" EXACT PSI-MI-alternate [] synonym: "n-terminal " EXACT PSI-MI-short [] synonym: "n-terminus" EXACT PSI-MI-alternate [] is_a: MI:0333 ! feature range status [Term] id: MI:0341 name: ragged n-terminus def: "Mixture of protein forms where N-terminus has been progressively truncated." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0340 ! n-terminal position [Term] id: MI:0342 name: sample process def: "Indicates the sample context in which each interacting molecule is presented to its partner." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0346 ! experimental preparation [Term] id: MI:0343 name: cdna library def: "Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process." [PMID:6110205] subset: PSI-MI_slim is_a: MI:0342 ! sample process [Term] id: MI:0344 name: cell lysate def: "Cell has been physically or chemically broken open and molecule present in resulting mixture of cellular components." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0342 ! sample process [Term] id: MI:0345 name: author assigned name def: "Name assigned to a molecule by the authors within a paper that may differ from the reference database." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1041 ! synonym [Term] id: MI:0346 name: experimental preparation def: "Set of terms to describe the participant experimental treatment and status. This term groups a number of orthologous short controlled vocabularies delivery method, expression level, molecular source, and sample process. Each participant can then be annotated with a maximum of 4 terms selected from each short list." [PMID:14755292] subset: PSI-MI_slim synonym: "experimental prep" EXACT PSI-MI-short [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0348 name: fixed cell def: "Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0342 ! sample process [Term] id: MI:0349 name: living cell def: "Molecule is observed within in a living cell." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0342 ! sample process [Term] id: MI:0350 name: purified def: "Molecule has undergone one or more purification steps to isolate it from the cellular environment." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0342 ! sample process [Term] id: MI:0351 name: homogeneous def: "The author states a molecule is completely pure, i.e. no other molecular species are present." [PMID:14755292] subset: PSI-MI_slim synonym: "pure" EXACT PSI-MI-alternate [] is_a: MI:0350 ! purified [Term] id: MI:0352 name: partially purified def: "The author states a molecule is only partially purified, i.e. other molecular species also known to be present." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0350 ! purified [Term] id: MI:0353 name: cross-reference type def: "Qualifier to describe the type of information a cross-reference is pointing to." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "CvXrefQualifier" EXACT PSI-MI-alternate [] synonym: "refType" EXACT PSI-MI-alternate [] synonym: "xref type" EXACT PSI-MI-short [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0354 name: cellular component def: "Cross reference pointing to a Gene Ontology -'cellular component' term." [PMID:14681407] subset: PSI-MI_slim synonym: "component" EXACT PSI-MI-short [] synonym: "go component term" EXACT PSI-MI-alternate [] xref: search-url: "https://www.ebi.ac.uk/QuickGO/term/${ac}" is_a: MI:0353 ! cross-reference type [Term] id: MI:0355 name: molecular function def: "Cross reference pointing to a Gene Ontology -'molecular function' term." [PMID:14681407] subset: PSI-MI_slim synonym: "function" EXACT PSI-MI-short [] synonym: "go function term" EXACT PSI-MI-alternate [] xref: search-url: "https://www.ebi.ac.uk/QuickGO/term/${ac}" is_a: MI:0353 ! cross-reference type [Term] id: MI:0356 name: identical object in an external resource def: "Reference to the corresponding object in another database. Correspondence may be complete or partial." [PMID:14755292] comment: For instance this qualifier, in an interaction entry, can be associated to a cross reference to the same interaction in an other database. subset: Drugable subset: PSI-MI_slim synonym: "identity" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0357 name: method reference def: "Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0358 name: primary-reference def: "Used to indicate the PMID from which the experimental data is extracted." [PMID:14755292] subset: Drugable subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0359 name: biological process def: "Cross reference pointing to a Gene Ontology -'cellular process' term." [PMID:14681407] subset: PSI-MI_slim synonym: "go process term" EXACT PSI-MI-alternate [] synonym: "process" EXACT PSI-MI-short [] xref: search-url: "https://www.ebi.ac.uk/QuickGO/term/${ac}" is_a: MI:0353 ! cross-reference type [Term] id: MI:0360 name: secondary accession number def: "Reference to the corresponding object in another database (like identity xref qualifier) but the identifier used in the external database is a secondary identifier or former accession number." [PMID:14755292] subset: PSI-MI_slim synonym: "secondary-ac" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0361 name: additional information def: "Related object within the same database or pointing to an external database." [PMID:14755292] subset: PSI-MI_slim synonym: "see-also" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0362 name: inference def: "Evidence based on human assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences." [PMID:14755292] subset: PSI-MI_slim synonym: "modeled" EXACT PSI-MI-alternate [] synonym: "modelled" EXACT PSI-MI-alternate [] is_a: MI:0001 ! interaction detection method is_a: MI:0002 ! participant identification method is_a: MI:0003 ! feature detection method [Term] id: MI:0363 name: inferred by author def: "Evidence based on the author of a paper assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences." [PMID:14755292] subset: PSI-MI_slim synonym: "modeled by author" EXACT PSI-MI-alternate [] synonym: "modelled by author" EXACT PSI-MI-alternate [] is_a: MI:0362 ! inference [Term] id: MI:0364 name: inferred by curator def: "Evidence based on a curator assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences." [PMID:14755292] subset: PSI-MI_slim synonym: "modeled by curator" EXACT PSI-MI-alternate [] synonym: "modelled by curator" EXACT PSI-MI-alternate [] is_a: MI:0362 ! inference [Term] id: MI:0365 name: enzyme tag def: "Molecule under study is fused to an enzyme, for example alkaline phosphatase, and measure of enzyme activity can be taken as indicative of presence of protein." [PMID:10935637] subset: PSI-MI_slim is_a: MI:0240 ! fusion protein [Term] id: MI:0366 name: alkaline phosphatase tag def: "Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein." [PMID:10935637] subset: PSI-MI_slim synonym: "alk phosphatase tag" EXACT PSI-MI-short [] is_a: MI:0365 ! enzyme tag [Term] id: MI:0367 name: green fluorescent protein tag def: "The green fluorescent protein of organisms such as the bioluminescent jellyfish Aequorea victoria can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." [PMID:7491768] subset: PSI-MI_slim synonym: "GFP" EXACT PSI-MI-alternate [] synonym: "gfp tag" EXACT PSI-MI-short [] synonym: "green fluorescent protein" EXACT PSI-MI-alternate [] is_a: MI:0687 ! fluorescent protein tag [Term] id: MI:0368 name: yellow fluorescent protein tag def: "Yellow fluorescent protein from species such as Vibrio fischeri can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." [PMID:10929120] subset: PSI-MI_slim synonym: "yellow fluorescent protein" EXACT PSI-MI-alternate [] synonym: "YFP" EXACT PSI-MI-alternate [] synonym: "yfp tag" EXACT PSI-MI-short [] is_a: MI:0687 ! fluorescent protein tag [Term] id: MI:0369 name: lex-a dimerization assay def: "The method is based on the repression of a reporter gene activity by two LexA DNA binding domains with different binding specificities. LexA is a transcription factor with an N-terminal DNA binding/activation domain (DBAct) and a C-terminal dimerization domain. LexA dimerization is required to repress transcription efficiently. The discovery of LexA DNA binding domains that bind to different DNA sequence enabled the development of this system." [PMID:12446730] subset: PSI-MI_slim synonym: "gallex" EXACT PSI-MI-alternate [] synonym: "gallex" EXACT PSI-MI-short [] is_a: MI:0232 ! transcriptional complementation assay [Term] id: MI:0370 name: tox-r dimerization assay def: "This assay allow identification of interactions in the inner membrane of E. coli. by using a chimeric construct ToxR-TM-MBP composed of the N-terminal DNA binding/transcriptional activation domain of ToxR (a dimerization dependant transcription factor) fused to a transmembrane domain of interest (TM) and a monomeric periplasmic anchor (the maltose binding protein). Association of the two TM results in the ToxR-mediated activation of a reporter gene such as CAT (chloroamphenicol acetyltransferase activity). The level of CAT expression indicates the strength of TM association. CAT expression can then be tested and quantify by measuring CAM resistance with disk diffusion assay or CAT activity assays on cell-free extracts." [PMID:9927659] subset: PSI-MI_slim synonym: "toxcat" EXACT PSI-MI-alternate [] synonym: "toxcat" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0371 name: 35s radiolabel def: "Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium." [PMID:14755292] subset: PSI-MI_slim synonym: "35S" EXACT PSI-MI-alternate [] synonym: "S35" EXACT PSI-MI-alternate [] synonym: "s35 radiolabelled" EXACT PSI-MI-alternate [] is_a: MI:0517 ! radiolabel [Term] id: MI:0372 name: subcellular preparation def: "Cell lysates are partially fractionated to isolate a specific subcellular fraction." [PMID:14755292] subset: PSI-MI_slim synonym: "subcellular prep" EXACT PSI-MI-short [] is_a: MI:0344 ! cell lysate [Term] id: MI:0373 name: dye label def: "Dye coupled to a molecule allowing its identification isolation and monitoring." [PMID:14577292] subset: PSI-MI_slim synonym: "dye labelled" EXACT PSI-MI-short [] is_a: MI:0505 ! experimental feature [Term] id: MI:0374 name: cyanine label def: "The organic polymethine cyanine dyes which, depending on structure, cover the spectrum from IR to UV.s. Their emission range is such that background fluorescence is often reduced. In addition these molecules can be linked directly to specific locations in synthetically produced nucleic acids." [PMID:14577292] subset: PSI-MI_slim is_a: MI:0373 ! dye label is_a: MI:0857 ! fluorescent dye label [Term] id: MI:0375 name: cy3 label def: "The organic cyanine Cy3 emits maximally at 570 nm." [PMID:14577292] subset: PSI-MI_slim is_a: MI:0374 ! cyanine label [Term] id: MI:0376 name: cy5 label def: "The organic cyanine Cy5 emits maximally at 670 nm." [PMID:14577292] subset: PSI-MI_slim is_a: MI:0374 ! cyanine label [Term] id: MI:0377 name: fluorescein isothiocyanate label def: "Fluorescein isothiocyanate is a yellow-green coloured low molecular weight dye which couples to proteins via reaction with primary amine groups at high pH. FITC is excitable at 488nm, close to its absorption maximum at 494nm, and produces maximum fluorescence emission around 520nm." [PMID:14577292] subset: PSI-MI_slim synonym: "FITC labelled" EXACT PSI-MI-alternate [] synonym: "fitc labelled" EXACT PSI-MI-short [] synonym: "fluorescein isothiocyanate labbeled" EXACT PSI-MI-alternate [] is_a: MI:0939 ! fluorescein label [Term] id: MI:0378 name: rare isotope label def: "Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule." [PMID:14577292] subset: PSI-MI_slim synonym: "rare isotope label" EXACT PSI-MI-short [] is_a: MI:0253 ! isotope label [Term] id: MI:0379 name: 13c label def: "Molecules labelled with isotope 13 of carbon atoms." [PMID:14577292] subset: PSI-MI_slim synonym: "13C" EXACT PSI-MI-alternate [] synonym: "C13" EXACT PSI-MI-alternate [] is_a: MI:0378 ! rare isotope label [Term] id: MI:0380 name: 15n label def: "Molecules labelled with isotope 15 of nytrogen atoms." [PMID:14577292] subset: PSI-MI_slim synonym: "15N" EXACT PSI-MI-alternate [] synonym: "N15" EXACT PSI-MI-alternate [] is_a: MI:0378 ! rare isotope label [Term] id: MI:0381 name: 2h label def: "Molecules labelled with isotope 2 of hydrogen atoms." [PMID:14577292] subset: PSI-MI_slim synonym: "2H2" EXACT PSI-MI-alternate [] synonym: "D2" EXACT PSI-MI-alternate [] synonym: "deuterium" EXACT PSI-MI-alternate [] is_a: MI:0378 ! rare isotope label [Term] id: MI:0382 name: mutation increasing interaction def: "Region of a molecule whose mutation or deletion increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction)." [PMID:14577292] subset: PSI-MI_slim synonym: "mutation increasing" EXACT PSI-MI-short [] is_a: MI:0118 ! mutation [Term] id: MI:0383 name: biopolymer def: "Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds." [PMID:14577292] subset: PSI-MI_slim is_a: MI:0313 ! interactor type [Term] id: MI:0384 name: alexa label def: "All Alexa dyes are fluorescent iodoacetamide dyes that can be conjugated with the primary amines of biomolecules. All Alexa dyes and their conjugates are more fluorescent and more photostable than the commonly used dyes. The numbers in the Alexa names indicate the approximate excitation wavelength maximum in nm)." [PMID:10449539] subset: PSI-MI_slim is_a: MI:0857 ! fluorescent dye label [Term] id: MI:0385 name: alexa 350 label def: "Alexa fluorescent dye analogue to AMCA (7-amino-4-methylcoumarin-3-acetic acid) with an approximate excitation wavelength maximum of 350 nm." [PMID:10449539] subset: PSI-MI_slim is_a: MI:0384 ! alexa label [Term] id: MI:0386 name: alexa 430 label def: "Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm." [PMID:10449539] subset: PSI-MI_slim is_a: MI:0384 ! alexa label [Term] id: MI:0387 name: alexa 488 label def: "Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm." [PMID:10449539] subset: PSI-MI_slim is_a: MI:0384 ! alexa label [Term] id: MI:0388 name: alexa 532 label def: "Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm." [PMID:10449539] subset: PSI-MI_slim is_a: MI:0384 ! alexa label [Term] id: MI:0389 name: alexa 546 label def: "Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm." [PMID:10449539] subset: PSI-MI_slim is_a: MI:0384 ! alexa label [Term] id: MI:0390 name: alexa 568 label def: "Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm." [PMID:10449539] subset: PSI-MI_slim is_a: MI:0384 ! alexa label [Term] id: MI:0391 name: alexa 594 label def: "Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm." [PMID:10449539] subset: PSI-MI_slim is_a: MI:0384 ! alexa label [Term] id: MI:0396 name: predetermined participant def: "Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s)." [PMID:14755292] subset: PSI-MI_slim synonym: "predetermined" EXACT PSI-MI-short [] is_a: MI:0661 ! experimental participant identification [Term] id: MI:0397 name: two hybrid array def: "Two-hybrid screening can be done in a colony array format, in which each colony expresses a defined pair of proteins. Because the particular protein pair expressed in each colony is defined by its position in the array, positive signals identify interacting proteins without further characterization, thus obviating the need for DNA purification and sequencing. The interrogation of a two-hybrid colony array usually involves a mating strategy in which every DNA binding domain hybrid (the bait) is tested against all activation domain hybrids (the preys) in a grid pattern. Arrays usually use full-length open reading frames." [PMID:11827624, PMID for application instance:10688190] subset: PSI-MI_slim is_a: MI:0018 ! two hybrid [Term] id: MI:0398 name: two hybrid pooling approach def: "In the pooling strategy sets of either both bait and prey hybrid vectors are mated or, more commonly, individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners. The pooling of both baits and prey molecules is now a rarely used technique as the pooling of baits often leads to misleading results." [PMID:11283351, PMID:20946815] subset: PSI-MI_slim synonym: "two hybrid pooling" EXACT PSI-MI-short [] is_a: MI:0018 ! two hybrid [Term] id: MI:0399 name: two hybrid fragment pooling approach def: "Individual baits are mated against pools of random fragmented preys. The usage of degenerated fragment allows identification of the minimal protein region required for the interaction. Since multiple clones that encode overlapping regions of protein are often identified, the minimal domain for interaction may be readily apparent from the initial screen." [PMID:12634794] subset: PSI-MI_slim synonym: "2h fragment pooling" EXACT PSI-MI-short [] is_a: MI:1112 ! two hybrid prey pooling approach [Term] id: MI:0400 name: affinity technology def: "Techniques which depend upon the strength of the interaction between two entities." [PMID:14755292] subset: PSI-MI_slim synonym: "affinity techniques" EXACT PSI-MI-short [] is_a: MI:0401 ! biochemical [Term] id: MI:0401 name: biochemical def: "The application of chemical principles and methods to biological experiments to demonstrate an interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0045 ! experimental interaction detection [Term] id: MI:0402 name: chromatin immunoprecipitation assay def: "Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. An antibody against a protein suspected of binding a given cis-element is used to immunoprecipitate fragmented chromatin fragments. Cells or tissue may first be briefly treated with an agent such formaldehyde to crosslink proteins to DNA. Nucleic acids are then identified by sequencing, for example polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element or next-generation sequencing techniques" [PMID:12054902] subset: PSI-MI_slim synonym: "ch-ip" EXACT PSI-MI-short [] is_a: MI:0019 ! coimmunoprecipitation [Term] id: MI:0403 name: colocalization def: "Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0190 ! interaction type [Term] id: MI:0404 name: comigration in non denaturing gel electrophoresis def: "comigration by non denaturing gel electrophoresis." [PMID:14755292] subset: PSI-MI_slim synonym: "comig non denat gel" EXACT PSI-MI-short [] is_a: MI:0807 ! comigration in gel electrophoresis [Term] id: MI:0405 name: competition binding def: "Competitive binding experiments measure equilibrium binding of a single concentration of ligand at various concentrations of an unlabeled competitor. Analysis of these data gives the affinity of the receptor for the competitor." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0400 ! affinity technology [Term] id: MI:0406 name: deacetylase assay def: "Measures the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study [Term] id: MI:0407 name: direct interaction def: "Interaction between molecules that are in direct contact with each other." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0915 ! physical association [Term] id: MI:0408 name: disulfide bond def: "Covalent bond mediated by 2 sulfur atoms." [PMID:14755292] subset: PSI-MI_slim synonym: "disulfide bridge" EXACT PSI-MI-alternate [] synonym: "SS-bond" EXACT PSI-MI-alternate [] is_a: MI:0195 ! covalent binding [Term] id: MI:0409 name: dna footprinting def: "Experimental method used to identify the region of a nucleic acid involved in an interaction with a protein. One sample of a radiolabeled nucleic acid of known sequence is submitted to partial digestion. A second sample is incubated with its interacting partner and then is submitted to the same partial digestion. The two samples are then analyzed in parallel by electrophoresis on a denaturing acrylamide gel. After autoradiography the identification of the bands that correspond to fragments missing from the lane loaded with the second sample reveals the region of the nucleic acid that is protected from nuclease digestion upon binding.\nOBSOLETE because redundant with MI:0417 'footprinting' combined with interactor type MI:0319 'DNA' \nreplace by:MI:0417" [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0410 name: electron tomography def: "Electron tomography is a general method for three-dimensional (3D) reconstruction of single, transparent objects from a series of projection images (i.e. from a tilt series) recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution." [PMID:12160704] subset: PSI-MI_slim synonym: "electron tomog" EXACT PSI-MI-short [] is_a: MI:0040 ! electron microscopy [Term] id: MI:0411 name: enzyme linked immunosorbent assay def: "Following non-covalent binding of a purified primary ligand to a solid phase, a blocking reagent is added to prevent any non-specific binding. A specific antigen is then allowed to bind to the primary ligand. Unbound antigen is removed by washing and a secondary antibody conjugated to an enzyme (e.g. horseradish peroxidase) is added. Following a washing step to remove unbound secondary ligand, the extent to which a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme in a given time is determined by spectrophotometry using a standard microplate absorbance reader. A similar type of approach can be utilized to detect enzymatic activities. The substrate, attached to a solid phase is incubated in the presence of the enzyme and the enzymatic modification is monitored by an antibody that is specific for the modified substrate (for instance a phosphorylated protein)." [PMID:11906746] subset: PSI-MI_slim synonym: "ELISA" EXACT PSI-MI-alternate [] synonym: "elisa" EXACT PSI-MI-short [] is_a: MI:0421 ! identification by antibody is_a: MI:0892 ! solid phase assay [Term] id: MI:0412 name: electrophoretic mobility supershift assay def: "The EMSA supershift is a EMSA experiment carried out using a third lane loaded with the radiolabeled nucleic acid, a protein mixture and an antibody for a specific protein. If an extra retardation is observed, this is due to the formation of a larger complex including the antibody. By this approach, at least one protein of the complex is directly identified." [PMID:12169687] subset: PSI-MI_slim synonym: "emsa supershift" EXACT PSI-MI-short [] is_a: MI:0413 ! electrophoretic mobility shift assay [Term] id: MI:0413 name: electrophoretic mobility shift assay def: "This method proves the interaction between a nucleic acid and a protein partner. On the same electrophoresis gel 1 lane is loaded with a nucleic acid of known sequence, a second lane is loaded with the same nucleic acid together with a purified protein (or a protein mixture). The nucleic acid is often radio-labelled to enable visualisation by autoradiography. Comparison of the nucleic acid migration in the two lanes enables the retardation of the nucleic acid due to its interaction with a protein to be observed." [PMID:12169687] subset: PSI-MI_slim synonym: "band shift" EXACT PSI-MI-alternate [] synonym: "emsa" EXACT PSI-MI-short [] synonym: "Gel retardation assay" EXACT PSI-MI-alternate [] is_a: MI:0807 ! comigration in gel electrophoresis [Term] id: MI:0414 name: enzymatic reaction def: "terms aiming to represent biochemical reactions referring to their resulting product modifications." [PMID:14755292] subset: PSI-MI_slim synonym: "Biochemical reaction" EXACT PSI-MI-alternate [] is_a: MI:0407 ! direct interaction [Term] id: MI:0415 name: enzymatic study def: "Participants are enzyme or substrate in a biochemical reaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0401 ! biochemical [Term] id: MI:0416 name: fluorescence microscopy def: "Fluorescent microscopy uses a high intensity light to illuminate the sample. This light excites fluorescence species in the sample, which then emit light of a longer wavelength. A fluorescent microscope also produces a magnified image of the sample, but the image is based on the second light source -- the light emanating from the fluorescent species -- rather than from the light originally used to illuminate, and excite, the sample." [PMID:14755292] subset: PSI-MI_slim synonym: "fluorescence imaging" EXACT PSI-MI-short [] is_a: MI:0428 ! imaging technique [Term] id: MI:0417 name: footprinting def: "Footprinting analysis is used to identify regions of molecules involved in binding other macromolecules and therefore protected from the effects of degradative enzymes, chemical treatment or other deleterious treatments." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0401 ! biochemical [Term] id: MI:0418 name: genetic def: "methods supporting genetic interactions.\nOBSOLETE as too unspecific use Genetic interference instead MI:0254." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0419 name: gtpase assay def: "Measures the catalysis of the reaction: GTP + H2O = GDP + phosphate." [PMID:14755292] subset: PSI-MI_slim synonym: "gtp hydrolisis" EXACT PSI-MI-alternate [] synonym: "GTPase" EXACT PSI-MI-alternate [] is_a: MI:0879 ! nucleoside triphosphatase assay [Term] id: MI:0420 name: kinase homogeneous time resolved fluorescence def: "Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being added from close proximity on the phosphorylated substrate due to the action of the kinase." [PMID:14987100] subset: PSI-MI_slim synonym: "homogeneous time-resolved fluorescence" EXACT PSI-MI-alternate [] synonym: "kinase HTRF" EXACT PSI-MI-alternate [] synonym: "kinase htrf" EXACT PSI-MI-short [] is_a: MI:0424 ! protein kinase assay is_a: MI:0510 ! homogeneous time resolved fluorescence [Term] id: MI:0421 name: identification by antibody def: "Antibody mediated participant identification." [PMID:14755292] subset: PSI-MI_slim synonym: "antibody detection" EXACT PSI-MI-short [] is_a: MI:0661 ! experimental participant identification [Term] id: MI:0422 name: immunostaining def: "Method using an antibody coupled with some colouring agent to detect a specific protein within a cell or tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0421 ! identification by antibody [Term] id: MI:0423 name: in-gel kinase assay def: "Substrate protein radio-labelled by kinase transferring an isotope of phosphate from the nucleotide. Substrate isolated by gel electrophoresis and radio-labelling confirmed by autoradiography." [PMID:14755292] subset: PSI-MI_slim synonym: "in gel kinase assay" EXACT PSI-MI-short [] is_a: MI:0424 ! protein kinase assay [Term] id: MI:0424 name: protein kinase assay def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0841 ! phosphotransferase assay [Term] id: MI:0425 name: kinase scintillation proximity assay def: "Relies on the radiolabelling of a peptide substrate immobilized on a scintillant coated SPA-bead. The kinase transfers a phosphate isotope from the nucleotide to the substrate." [PMID:14755292] subset: PSI-MI_slim synonym: "kinase spa" EXACT PSI-MI-short [] is_a: MI:0099 ! scintillation proximity assay is_a: MI:0424 ! protein kinase assay [Term] id: MI:0426 name: light microscopy def: "Light visible microscopy uses environmental light to illuminate the sample and produce a magnified image of the sample." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0428 ! imaging technique [Term] id: MI:0427 name: Identification by mass spectrometry def: "identification by mass spectrometry." [PMID:14755292] subset: PSI-MI_slim synonym: "ms participant" EXACT PSI-MI-short [] is_a: MI:0661 ! experimental participant identification [Term] id: MI:0428 name: imaging technique def: "Methods that provide images of molecules at various resolution depending on the technology used." [PMID:14755292] subset: PSI-MI_slim synonym: "microscopy" EXACT PSI-MI-alternate [] is_a: MI:0045 ! experimental interaction detection [Term] id: MI:0429 name: necessary binding region def: "A sequence range within a molecule identified as being absolutely required for an interaction. The sequence may or may not be in direct physical contact with the interaction partner." [PMID:14755292] subset: PSI-MI_slim synonym: "deletion disrupting interaction" EXACT [] synonym: "necessary binding site" EXACT [] synonym: "required to bind" EXACT PSI-MI-short [] is_a: MI:0117 ! binding-associated region is_a: MI:0573 ! mutation disrupting interaction is_a: MI:1128 ! mutation disrupting interaction strength is_a: MI:1129 ! mutation disrupting interaction rate [Term] id: MI:0430 name: nucleic acid uv cross-linking assay def: "Nucleic acids are incubated with purified proteins or a protein mixture and then exposed to a chemical cross-linking agent that may be activated by UV light exposure. The eventual complexes can be identified by sequencing or autoradiography if the nucleic acid is radio-labelled and the sequence is known. The proteins involved in the complex can be recognized by specific antibodies or by retrieving the original protein mixture and carrying further analysis on it." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl ac uv crosslink" EXACT PSI-MI-short [] is_a: MI:0030 ! cross-linking study [Term] id: MI:0431 name: obsolete def: "Deprecated terms.\nOBSOLETE term replaced by the default OBO class 'Obsolete'." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0432 name: one hybrid def: "Protein-DNA complementation assay where a single promoter act as bait and is screened against a library of prey transcription factors." [PMID:10589421] subset: PSI-MI_slim synonym: "1 hybrid" EXACT PSI-MI-short [] synonym: "one-hybrid" EXACT PSI-MI-alternate [] synonym: "yeast one hybrid" EXACT PSI-MI-alternate [] synonym: "yeast one-hybrid" EXACT PSI-MI-alternate [] is_a: MI:0232 ! transcriptional complementation assay [Term] id: MI:0433 name: partial identification of protein sequence def: "partial protein sequence identification." [PMID:14755292] subset: PSI-MI_slim synonym: "partial id prot seq" EXACT PSI-MI-short [] is_a: MI:0093 ! protein sequence identification is_a: MI:0659 ! experimental feature detection [Term] id: MI:0434 name: phosphatase assay def: "Measures the catalysis of the reaction: a phosphosubstrate + H2O = a substrate + phosphate." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study [Term] id: MI:0435 name: protease assay def: "Measures the enzymatic hydrolysis of a peptide bond within a peptide or protein substrate." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0990 ! cleavage assay [Term] id: MI:0436 name: protein footprinting def: "Protein footprinting is a technique for identifying structural changes modulated by protein-ligand binding, and mapping protein-ligand interfaces This technique involves attaching cutting reagents randomly to amino acid residue (e.g. lysine or cysteine) on the proteins surface and then using this lysine-labelled protein to cleave polypeptide backbone of the other protein at exposed residues adjacent to its binding site." [PMID:14600024, PMID:14967031, PMID:14987073] subset: PSI-MI_slim is_a: MI:0659 ! experimental feature detection [Term] id: MI:0437 name: protein three hybrid def: "Two hybrid assay performed with a third protein component co-transfected into a recombinant yeast strain together with a bait and a prey construct. Negative control shows that the interaction between the bait and the prey do not occur when the third protein is not co-transfected." [PMID:12052864, PMID:12761205, PMID:12935900] subset: PSI-MI_slim synonym: "bridge assay" EXACT PSI-MI-alternate [] synonym: "protein 3-hybrid" EXACT PSI-MI-alternate [] synonym: "protein tri hybrid" EXACT PSI-MI-alternate [] synonym: "trihybrid" EXACT PSI-MI-alternate [] is_a: MI:0018 ! two hybrid is_a: MI:0588 ! three hybrid [Term] id: MI:0438 name: rna three hybrid def: "In vivo reconstruction of specific RNA-proteins interactions. The DNA binding and transcription activator domains of GAL4 are brought together via the interaction of recombinant RNA. The first hybrid protein contains the DNA binding domain of GAL4 fused to RevM10 (a mutated RNA binding protein of HIV-1 that binds specifically to the Rev responsive element RRE of the env gene). A recombinant RNA contains the RRE sequence and a target RNA sequence X. The second hybrid protein contains the activation domain of GAL4 fused to protein Y tested for its ability to bind the target RNA X. If this interaction occurs the three hybrid reconstructs GAL4 and the transcription of a reporter gene is activated." [PMID:12162957, PMID:8972875] subset: PSI-MI_slim synonym: "rna 3-hybrid" EXACT PSI-MI-alternate [] synonym: "rna tri hybrid" EXACT PSI-MI-alternate [] synonym: "rna-three hybrid" EXACT PSI-MI-alternate [] synonym: "Three hybrid system" EXACT PSI-MI-alternate [] is_a: MI:0588 ! three hybrid [Term] id: MI:0439 name: random spore analysis def: "A technique used to detect genetic interactions between 2 (or more) genes in a sporulating organism by scoring a large population of haploid spores for a phenotype and correlating the phenotype with the presence of single vs double (multiple) mutations. A diploid heterozygous organism harbouring mutations in two (or more) genes is induced to sporulate. Resulting spores are meiotic segregants that are haploid and are either wild type or mutant at each locus. Spores are scored for a phenotype, such as loss of viability." [PMID:14755292] subset: PSI-MI_slim synonym: "random-spore analysis" EXACT PSI-MI-alternate [] synonym: "RSA" EXACT PSI-MI-alternate [] synonym: "rsa" EXACT PSI-MI-short [] synonym: "spore germination" EXACT PSI-MI-alternate [] is_a: MI:0254 ! genetic interference [Term] id: MI:0440 name: saturation binding def: "Saturation binding experiments measure specific ligand binding at equilibrium at various concentrations of the ligand. Analysis of these data can determine receptor number and affinity." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0400 ! affinity technology [Term] id: MI:0441 name: synthetic genetic analysis def: "Identification of genetic interactions by generation of an organism harbouring mutations in 2 or more genes and scoring for a phenotype, such as loss of viability, that is not observed for any of the mutations in isolation." [PMID:14755292] subset: PSI-MI_slim synonym: "SGA" EXACT PSI-MI-alternate [] synonym: "sga" EXACT PSI-MI-short [] is_a: MI:0254 ! genetic interference [Term] id: MI:0442 name: sufficient binding region def: "Binding will occur when this sequence range is present within a molecule or part of a molecule. This region will contain the direct binding region but may be longer." [PMID:14755292] subset: PSI-MI_slim synonym: "sufficient binding site" EXACT [] synonym: "sufficient to bind" EXACT PSI-MI-short [] is_a: MI:0117 ! binding-associated region [Term] id: MI:0443 name: ubiquitin binding def: "Interaction concerning ubiquitin that is covalently attached to any Lys residue of its interaction partner.\nOBSOLETE remap to ubiquitination reaction (MI:0220) or describe ubiquitine as a participant on the interaction using physical interaction (MI:0218) or covalent binding (MI:0195) as interaction type." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0444 name: database citation def: "Database citation list names of databases commonly used to cross reference interaction data." [PMID:14755292] subset: Drugable subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0445 name: literature database def: "Databases acting as a source of literature information." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "experiment xref" EXACT PSI-MI-short [] is_a: MI:0444 ! database citation [Term] id: MI:0446 name: pubmed def: "PubMed is designed to provide access to citations from biomedical literature. The data can be found at both NCBI PubMed and Europe PubMed Central. \nhttp://www.ncbi.nlm.nih.gov/pubmed\nhttp://europepmc.org" [PMID:14755292] subset: Drugable subset: PSI-MI_slim xref: id-validation-regexp: "[0-9]+" xref: search-url: "http://europepmc.org/abstract/MED/${ac}" is_a: MI:0445 ! literature database [Term] id: MI:0447 name: feature database def: "A database describing a feature on a molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "feature xref" EXACT PSI-MI-short [] is_a: MI:0444 ! database citation [Term] id: MI:0448 name: gene ontology def: "The objective of Gene Ontology (GO) is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products.\nhttp://www.ebi.ac.uk/GO" [PMID:14755292] subset: PSI-MI_slim synonym: "go" EXACT PSI-MI-short [] xref: id-validation-regexp: "GO:[0-9]{7}" xref: search-url: "https://www.ebi.ac.uk/QuickGO/term/${ac}" is_a: MI:0447 ! feature database is_a: MI:0461 ! interaction database [Term] id: MI:0449 name: interpro def: "InterPro combines a number of databases (referred to as member databases) that use different methodologies and a varying degree of biological information on well-characterised proteins to derive protein signatures that predict family membership and domain composition of naive protein sequences.\nhttp://www.ebi.ac.uk/interpro/" [PMID:1252001] subset: PSI-MI_slim synonym: "InterPro" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "IPR[0-9]{6}" xref: search-url: "http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=${ac}" is_a: MI:0447 ! feature database [Term] id: MI:0450 name: cdd def: "The Conserved Domain Database may be used to identify the conserved domains present in a protein sequence.\nhttp://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml" [PMID:14755292] subset: PSI-MI_slim synonym: "CDD" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[0-9]+" is_a: MI:0447 ! feature database [Term] id: MI:0451 name: pfam def: "Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.\nhttp://www.sanger.ac.uk/Software/Pfam" [PMID:14755292] subset: PSI-MI_slim synonym: "Pfam" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "PF[0-9]{5}" is_a: MI:0449 ! interpro [Term] id: MI:0452 name: pirsf def: "PIRSF is a classification system based on evolutionary relationship of whole proteins.\nhttp://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml" [PMID:14755292] subset: PSI-MI_slim synonym: "PIRSF" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "PIRSF[0-9]{5}" is_a: MI:0449 ! interpro [Term] id: MI:0453 name: prints def: "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family.\nhttp://umber.sbs.man.ac.uk/dbbrowser/PRINTS/" [PMID:14755292] subset: PSI-MI_slim synonym: "PRINTS" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "PR[0-9]{6}" is_a: MI:0449 ! interpro [Term] id: MI:0454 name: prodom def: "The ProDom protein domain database consists of an automatic compilation of homologous domains.\nhttp://protein.toulouse.inra.fr/prodom.html" [PMID:14755292] subset: PSI-MI_slim synonym: "ProDom" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "PD[0-9]{6}" is_a: MI:0449 ! interpro [Term] id: MI:0455 name: prosite def: "PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles.\nhttp://us.expasy.org/prosite/" [PMID:14755292] subset: PSI-MI_slim synonym: "Prosite" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "PS[0-9]{5}" is_a: MI:0449 ! interpro [Term] id: MI:0456 name: scop superfamily def: "SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain.\nhttp://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/" [PMID:14755292] subset: PSI-MI_slim synonym: "SCOP superfamily" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[0-9]+" is_a: MI:0449 ! interpro [Term] id: MI:0457 name: smart def: "SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures.\nhttp://smart.embl-heidelberg.de/" [PMID:14755292] subset: PSI-MI_slim synonym: "SMART" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "SM[0-9]{5}" is_a: MI:0449 ! interpro [Term] id: MI:0458 name: tigrfams def: "TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, Hidden Markov Models (HMMs) and annotation.\nhttp://www.tigr.org/TIGRFAMs" [PMID:14755292] subset: PSI-MI_slim synonym: "TIGRFAMs" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "TIGR[0-9]+" is_a: MI:0449 ! interpro [Term] id: MI:0459 name: mmdb def: "MMDB (Molecular Modeling DataBase), is a subset of three-dimensional structures obtained from the Protein Data Bank.\nhttp://www.ncbi.nlm.nih.gov/Structure" [PMID:14755292] subset: PSI-MI_slim synonym: "MMDB" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[0-9]+" is_a: MI:0447 ! feature database is_a: MI:0461 ! interaction database [Term] id: MI:0460 name: rcsb pdb def: "The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. \nhttp://www.pdb.org/" [PMID:14634627] subset: Drugable subset: PSI-MI_slim synonym: "PDB" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[0-9][a-zA-Z0-9]{3}" xref: search-url: "http://www.pdb.org/pdb/explore/explore.do?structureId=${ac}" is_a: MI:0805 ! wwpdb [Term] id: MI:0461 name: interaction database def: "Databases that contain experimental or predictive molecular interaction data." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "interaction xref" EXACT PSI-MI-short [] is_a: MI:0444 ! database citation [Term] id: MI:0462 name: bind def: "The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions.\nhttp://www.blueprint.org/bind" [PMID:14755292] subset: PSI-MI_slim synonym: "BIND" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[0-9]+" is_a: MI:0461 ! interaction database is_a: MI:0489 ! source database [Term] id: MI:0463 name: biogrid def: "The General Repository for Interaction Datasets (BioGRID) is a database of genetic and physical interactions.\nhttp://thebiogrid.org" [PMID:21071413] subset: PSI-MI_slim synonym: "BioGRID" EXACT PSI-MI-alternate [] is_a: MI:0461 ! interaction database is_a: MI:0489 ! source database [Term] id: MI:0464 name: cygd def: "The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis.\nhttp://mips.gsf.de/proj/yeast/CYGD.\nhttp://mips.gsf.de/genre/proj/mpact" [PMID:14755292] subset: PSI-MI_slim synonym: "CYGD" EXACT PSI-MI-alternate [] synonym: "CYGD (MIPS)" EXACT PSI-MI-alternate [] synonym: "MIPS" EXACT PSI-MI-alternate [] synonym: "MPact" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[0-9]+|[A-Z]{3}[0-9]{3}[A-Za-z](-[A-Za-z])?|[A-Z0-9]+\\.[0-9]+|YM[A-Z][0-9]{3}[a-z][0-9]" is_a: MI:0489 ! source database is_a: MI:1094 ! genome databases is_a: MI:1106 ! pathways database [Term] id: MI:0465 name: dip def: "The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.\nhttp://dip.doe-mbi.ucla.edu/" [PMID:14755292] subset: PSI-MI_slim synonym: "DIP" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "DIP[0-9]+[NE]" xref: search-url: "http://identifiers.org/dip/" is_a: MI:0461 ! interaction database is_a: MI:0973 ! imex source [Term] id: MI:0466 name: ecocyc def: "EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli K12 MG1655.\nhttp://ecocyc.org/" [PMID:14755292] subset: PSI-MI_slim synonym: "EcoCyc" EXACT PSI-MI-alternate [] is_a: MI:1106 ! pathways database [Term] id: MI:0467 name: reactome def: "The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology.\nhttp://www.reactome.org/" [PMID:21067998] subset: PSI-MI_slim synonym: "Genome Knowledge Base" EXACT PSI-MI-alternate [] synonym: "GKB" EXACT PSI-MI-alternate [] synonym: "Reactome" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "REACT_\\d+(\\.\\d+)?$" xref: search-url: "http://www.reactome.org/content/detail/${ac}" is_a: MI:1106 ! pathways database [Term] id: MI:0468 name: hprd def: "The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.\nhttp://www.hprd.org/" [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "HPRD" EXACT PSI-MI-alternate [] is_a: MI:0461 ! interaction database [Term] id: MI:0469 name: intact def: "INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions.\nhttp://www.ebi.ac.uk/intact" [PMID:14681455, PMID:19850723, PMID:22121220] subset: PSI-MI_slim synonym: "IntAct" EXACT PSI-MI-short [] xref: id-validation-regexp: "EBI-[0-9]+|IA:[0-9]+" xref: search-url: "http://www.ebi.ac.uk/intact/query/${ac}" is_a: MI:0461 ! interaction database is_a: MI:0973 ! imex source [Term] id: MI:0470 name: kegg def: "KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information and also supplies information about chemical compounds, enzyme molecules and enzymatic reactions.\nhttp://www.genome.ad.jp/kegg/" [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "KEGG" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[a-zA-Z]+:[a-zA-Z]+[0-9]+" is_a: MI:0473 ! participant database is_a: MI:1106 ! pathways database [Term] id: MI:0471 name: mint def: "The Molecular INTeraction database (MINT) is a relational database designed to store interactions between biological molecules.\nhttp://mint.bio.uniroma2.it" [PMID:14755292] subset: PSI-MI_slim synonym: "MINT" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "MINT-[0-9]+" is_a: MI:0461 ! interaction database is_a: MI:0973 ! imex source [Term] id: MI:0472 name: pdbe def: "The Protein Data Bank in Europe - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB).\nhttp://www.ebi.ac.uk/pdbe/" [PMID:16381867] subset: PSI-MI_slim synonym: "e-MSD" EXACT [] synonym: "MSD" RELATED [] synonym: "PQS" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[0-9][a-zA-Z0-9]{3}" xref: search-url: "http://www.ebi.ac.uk/pdbe/entry/pdb/${ac}" is_a: MI:0805 ! wwpdb [Term] id: MI:0473 name: participant database def: "Database of molecules participating in molecular interactions." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "participant xref" EXACT PSI-MI-short [] is_a: MI:0444 ! database citation [Term] id: MI:0474 name: chebi def: "A definitive, freely available database of Chemical compounds of Biological Interest (ChEBI).\nhttp://www.ebi.ac.uk/chebi/" [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "ChEBI" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "CHEBI:[0-9]+" xref: search-url: "http://www.ebi.ac.uk/chebi/searchId.do?chebiId=${ac}" is_a: MI:2054 ! bioactive entity reference [Term] id: MI:0475 name: ddbj/embl/genbank def: "DDBJ EMBL GenBank Nucleotide Sequence Database Collaboration exchange new and updated data on a daily basis to achieve optimal synchronisation.\nhttp://www.ebi.ac.uk/embl/Contact/collaboration" [PMID:14755292] subset: PSI-MI_slim synonym: "DDBJ" EXACT PSI-MI-alternate [] synonym: "DDBJ/EMBL/GenBank" EXACT PSI-MI-alternate [] synonym: "EMBL" EXACT PSI-MI-alternate [] synonym: "GenBank" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[A-Z][0-9]{5}|[A-Z][0-9]{5}\\.[0-9]+|[A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\\.[0-9]+|[A-Z]{4}[0-9]{8}|[A-Z]{4}[0-9]{8}\\.[0-9]+" xref: search-url: "http://www.ebi.ac.uk/cgi-bin/dbfetch?db=EMBLSVA&id=${ac}" is_a: MI:0683 ! sequence database [Term] id: MI:0476 name: ensembl def: "Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes.\nhttp://www.ensembl.org" [PMID:15078858] subset: PSI-MI_slim synonym: "Ensembl" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "ENS[A-Z]+[0-9]{11}|[A-Z]{3}[0-9]{3}[A-Za-z](-[A-Za-z])?|CG[0-9]+|[A-Z0-9]+\\.[0-9]+|YM[A-Z][0-9]{3}[a-z][0-9]" xref: search-url: "http://www.ensembl.org/Multi/Search/Results?q=${ac}" is_a: MI:1094 ! genome databases [Term] id: MI:0477 name: entrez gene/locuslink def: "LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci.\nhttp://www.ncbi.nlm.nih.gov/LocusLink/" [PMID:14755292] subset: PSI-MI_slim synonym: "Entrez gene/locuslink" EXACT PSI-MI-alternate [] synonym: "entrezgene/locuslink" EXACT PSI-MI-short [] xref: id-validation-regexp: "[0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+" is_a: MI:1109 ! gene database [Term] id: MI:0478 name: flybase def: "FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila.\nhttp://flybase.org" [PMID:14755292] subset: PSI-MI_slim synonym: "FlyBase" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "FB[a-z]{2}[0-9]{7}" xref: search-url: "http://flybase.org/reports/${ac}" is_a: MI:1094 ! genome databases [Term] id: MI:0479 name: mgd/mgi def: "Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.\nhttp://www.informatics.jax.org/" [PMID:14755292] subset: PSI-MI_slim synonym: "MGD/MGI" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "MGI:[0-9]+" is_a: MI:1094 ! genome databases [Term] id: MI:0480 name: omim def: "Online Mendelian Inheritance in Man (OMIM) is a catalogue of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases.\nhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM" [PMID:14755292] subset: PSI-MI_slim synonym: "OMIM" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[0-9]+" xref: search-url: "http://www.omim.org/entry/${ac}" is_a: MI:0683 ! sequence database [Term] id: MI:0481 name: refseq def: "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for a number of organisms.\nhttp://www.ncbi.nlm.nih.gov/RefSeq/" [PMID:14755292] subset: PSI-MI_slim synonym: "Refseq" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[XNZ][A-Z]_[0-9]+|[0-9]+|[XNZ][A-Z]_[0-9]+\\.[0-9]+" is_a: MI:1096 ! protein sequence databases [Term] id: MI:0482 name: rfam def: "Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families.\nhttp://www.sanger.ac.uk/Software/Rfam/" [PMID:14755292] subset: PSI-MI_slim synonym: "rfam" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "RF[0-9]{5}" is_a: MI:0683 ! sequence database [Term] id: MI:0483 name: rgd def: "The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data.\nhttp://rgd.mcw.edu/" [PMID:14755292] subset: PSI-MI_slim synonym: "RGD" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[0-9]+" is_a: MI:1094 ! genome databases [Term] id: MI:0484 name: sgd def: "SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae.\nhttp://www.yeastgenome.org/" [PMID:14755292] subset: PSI-MI_slim synonym: "Saccharomyces Genome Database" EXACT PSI-MI-alternate [] synonym: "SGD" EXACT PSI-MI-short [] xref: id-validation-regexp: "S[0-9]{9}" xref: search-url: "http://www.yeastgenome.org/locus/${ac}/overview" is_a: MI:1094 ! genome databases [Term] id: MI:0485 name: uniparc def: "UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences derived from many sources.\nhttp://www.ebi.ac.uk/uniparc/" [PMID:14681372] subset: PSI-MI_slim synonym: "UniParc" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "UPI[A-F0-9]{10}" xref: search-url: "http://www.ebi.uniprot.org/entry/${ac}" is_a: MI:1097 ! uniprot [Term] id: MI:0486 name: uniprot knowledge base def: "UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.\nhttp://www.uniprot.org" [PMID:14681372] subset: PSI-MI_slim synonym: "uniprotkb" EXACT PSI-MI-short [] synonym: "UniProtKB" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}-PRO_[0-9]{10}" xref: search-url: "http://www.uniprot.org/uniprot/${ac}" is_a: MI:0461 ! interaction database is_a: MI:0973 ! imex source is_a: MI:1097 ! uniprot [Term] id: MI:0487 name: wormbase def: "WormBase is the central worm database that houses the gene reports, locus reports, translation reports, expression pattern data and genome browser.\nhttp://www.wormbase.org/" [PMID:14755292] subset: PSI-MI_slim synonym: "WormBase" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "WBGene[0-9]{8}" is_a: MI:1094 ! genome databases [Term] id: MI:0488 name: psi-mi def: "PSI-MI." [PMID:14755292] subset: PSI-MI_slim synonym: "PSI-MI" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "MI:[0-9]{4}" xref: search-url: "http://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=${ac}" is_a: MI:0444 ! database citation [Term] id: MI:0489 name: source database def: "Database that originally provided the interaction record for exchange purposes." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0444 ! database citation [Term] id: MI:0490 name: experiment condition def: "Describes the location of the experiment.\nOBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0491 name: in silico def: "Results generated by predictive bioinformatics approaches rather than experimental data.\nOBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "Predictive" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0492 name: in vitro def: "Experiments performed with participants removed from the cellular environment e.g. cell extracts, isolated proteins.\nOBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0493 name: in vivo def: "Experiment undertaken within a cellular environment, although this may not be the natural host of the proteins in the study.\nOBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0494 name: in situ def: "Literally, in place i.e. the protein is in its natural environment during the experiment.\nOBSOLETE as a full host organisms is recommended using tax id == -1 as convention to refer to 'in vitro' interaction." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0495 name: experimental role def: "Role played by the participant within the experiment." [PMID:14755292] subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0496 name: bait def: "Molecule experimentally treated to capture its interacting partners." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role [Term] id: MI:0497 name: neutral component def: "Molecule role in an experimental setting that does not have an embedded asymmetry." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role [Term] id: MI:0498 name: prey def: "Molecule experimentally identified as being captured by a given bait." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role [Term] id: MI:0499 name: unspecified role def: "Role not specified or not applicable to the data." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role is_a: MI:0500 ! biological role [Term] id: MI:0500 name: biological role def: "Physiological role of an interactor in a cell or in vivo environment, which is reproduced in the current experiment." [PMID:14755292] subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0501 name: enzyme def: "Molecule catalyzing a modification on its interacting partner." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0500 ! biological role [Term] id: MI:0502 name: enzyme target def: "Molecule that is the target of its binding partner catalytic activity." [PMID:14755292] subset: PSI-MI_slim synonym: "substrate" EXACT PSI-MI-alternate [] is_a: MI:0500 ! biological role [Term] id: MI:0503 name: self def: "Molecule that makes intramolecular interactions." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role is_a: MI:0500 ! biological role [Term] id: MI:0505 name: experimental feature def: "The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0116 ! feature type [Term] id: MI:0506 name: over expressed level def: "A molecule is estimated to be expressed at higher levels than in physiological condition." [PMID:14755292] subset: PSI-MI_slim synonym: "over-expressed" EXACT PSI-MI-short [] is_a: MI:0221 ! expression level is_a: MI:0803 ! expression level alteration [Term] id: MI:0507 name: tag def: "Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labelled molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0505 ! experimental feature [Term] id: MI:0508 name: deacetylase radiometric assay def: "Measures the release of radiolabelled acetic acid from a pre-labeled molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "radiolabeled acetate" EXACT PSI-MI-short [] is_a: MI:0406 ! deacetylase assay [Term] id: MI:0509 name: phosphatase homogeneous time resolved fluorescence def: "Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being removed from close proximity on the phosphorylated substrate due to the action of the phosphatase." [PMID:14987100] subset: PSI-MI_slim synonym: "homogeneous time-resolved fluorescence" EXACT PSI-MI-alternate [] synonym: "phosphatase HTRF" EXACT PSI-MI-alternate [] synonym: "phosphatase htrf" EXACT PSI-MI-short [] is_a: MI:0434 ! phosphatase assay is_a: MI:0510 ! homogeneous time resolved fluorescence [Term] id: MI:0510 name: homogeneous time resolved fluorescence def: "Methods based on the exceptionally long fluorescence lifetime characteristics of certain fluorophores, which allows the elimination of the effects of background fluorescence. Uses nonradiative energy transfer or quenching between fluorescent lanthanide chelates and different acceptors to measure reaction rates." [PMID:14987100] subset: PSI-MI_slim synonym: "homogeneous time-resolved fluorescence" EXACT PSI-MI-alternate [] synonym: "htrf" EXACT PSI-MI-short [] is_a: MI:0051 ! fluorescence technology [Term] id: MI:0511 name: protease homogeneous time resolved fluorescence def: "Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Fluorescence donor and acceptor are on the same peptide molecule and separated by the action of the protease." [PMID:14987100] subset: PSI-MI_slim synonym: "Protease HTRF" EXACT PSI-MI-alternate [] synonym: "protease htrf" EXACT PSI-MI-short [] is_a: MI:0435 ! protease assay is_a: MI:0510 ! homogeneous time resolved fluorescence [Term] id: MI:0512 name: zymography def: "Samples run on a gelatine containing gels under non-reducing condition, gels then incubated under conditions in which the enzyme is active. Gels are stained with coomasie and gelatine-free regions of the gel taken as a measure of enzyme activity." [PMID:2071592] subset: PSI-MI_slim is_a: MI:0435 ! protease assay [Term] id: MI:0513 name: collagen film assay def: "Measures the amount of radiolabel released into the medium when enzyme is added onto a film of isotope-labelled collagen." [PMID:6247938] subset: PSI-MI_slim is_a: MI:0435 ! protease assay [Term] id: MI:0514 name: in gel phosphatase assay def: "Substrate pre-radiolabelled either synthetically or through the action of a kinase transferring an isotope of phosphate from a nucleotide. Substrate then exposed to phosphate under assay conditions. Substrate isolated by gel electrophoresis and loss of radiolabelling confirmed by autoradiography." [PMID:14755292] subset: PSI-MI_slim synonym: "in gel phosphatase" EXACT PSI-MI-short [] is_a: MI:0434 ! phosphatase assay [Term] id: MI:0515 name: methyltransferase assay def: "Measures the catalysis of the transfer of a methyl group to an acceptor molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "methyltransferase as" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study [Term] id: MI:0516 name: methyltransferase radiometric assay def: "Measures the transfer of a radiolabelled methyl group of a donor, for example S-adenosyl-L-methionine (SAM) to a carboxyl group of an acceptor." [PMID:14755292] subset: PSI-MI_slim synonym: "radiolabeled methyl" EXACT PSI-MI-short [] is_a: MI:0515 ! methyltransferase assay [Term] id: MI:0517 name: radiolabel def: "A radiolabelled molecule has radio isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "radiolabeled" EXACT PSI-MI-alternate [] synonym: "radiolabelled" EXACT PSI-MI-short [] is_a: MI:0253 ! isotope label [Term] id: MI:0518 name: flag tag def: "The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem." [PMID:14755292] subset: PSI-MI_slim synonym: "DYKDDDDKV epitope tag" EXACT PSI-MI-alternate [] synonym: "FLAG" EXACT PSI-MI-alternate [] synonym: "FLAG-tagged" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0519 name: glutathione s tranferase tag def: "The protein is expressed and purified as a fusion to the glutathione S-tranferase protein." [PMID:14755292] subset: PSI-MI_slim synonym: "glutathione S-tranferase tag" EXACT PSI-MI-alternate [] synonym: "gst tag" EXACT PSI-MI-short [] is_a: MI:0365 ! enzyme tag [Term] id: MI:0520 name: ha tag def: "The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemagglutinin protein) for which antibodies are commercially available." [PMID:14755292] subset: PSI-MI_slim synonym: "YPYDVPDYA epitope tag" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0521 name: his tag def: "The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies." [PMID:14755292] subset: PSI-MI_slim synonym: "6-His-tag" EXACT PSI-MI-alternate [] synonym: "Hexa-His-tag" EXACT PSI-MI-alternate [] synonym: "Histidine-tag" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0522 name: myc tag def: "The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem." [PMID:14755292] subset: PSI-MI_slim synonym: "EUKLISEED epitope tag" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0523 name: t7 tag def: "The protein of interest is expressed as a fusion to the peptide MASMTGGQQMG for which antibodies are commercially available." [PMID:14755292] subset: PSI-MI_slim synonym: "MASMTGGQQMG epitope tag" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0524 name: calmodulin binding peptide plus protein a tag def: "Tag encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A fused to a target protein. The tag allows two purification steps ensuring a highly selective purification of the tagged protein." [PMID:14755292] subset: PSI-MI_slim synonym: "CBP-ProtA tagged" EXACT PSI-MI-alternate [] synonym: "tap tagged" EXACT PSI-MI-short [] is_a: MI:0677 ! tandem tag [Term] id: MI:0525 name: v5 tag def: "The protein of interest is expressed as a fusion to the peptide GKPIPNPLLGLDST for which antibodies are commercially available." [PMID:14755292] subset: PSI-MI_slim synonym: "GKPIPNPLLGLDST epitope tag" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0526 name: n-acetyl-lysine def: "Residue modification.\nOBSOLETE remap to MOD:00723." [PMID:14755292, RESID:AA0048, RESID:AA0055] synonym: "acetyllysine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0527 name: adp ribosylated residue def: "Residue modification.\nOBSOLETE remap to MOD:00752." [PMID:14755292] synonym: "adp-ribosylated" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0528 name: omega-n-(adp-ribosyl)-arginine def: "Residue modification.\nOBSOLETE remap to MOD:00177." [PMID:14755292, RESID:AA0168] synonym: "(S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acid" EXACT PSI-MI-alternate [] synonym: "adp-ribosylarginine" EXACT PSI-MI-short [] synonym: "N(omega)-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-arginine" EXACT PSI-MI-alternate [] synonym: "N(omega)-alpha-D-ribofuranosyl-L-arginine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" EXACT PSI-MI-alternate [] synonym: "omega-N-(ADP-ribosyl)-L-arginine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0529 name: s-(adp-ribosyl)-cysteine def: "Residue modification.\nOBSOLETE remap to MOD:00178." [PMID:14755292, RESID:AA0169] synonym: "(R)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]sulfanyl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "adp-ribosylcysteine" EXACT PSI-MI-short [] synonym: "S-(ADP-ribosyl)-L-cysteine" EXACT PSI-MI-alternate [] synonym: "S-alpha-D-ribofuranosyl-L-cysteine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" EXACT PSI-MI-alternate [] synonym: "S-L-cysteine alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0530 name: glutamyl-5-poly(adp-ribose) def: "Residue modification.\nOBSOLETE remap to MOD:00300." [PMID:14755292, RESID:AA0295] synonym: "(S)-2-amino-5-poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl]oxy-5-oxopentanoic acid" EXACT PSI-MI-alternate [] synonym: "adp-ribosylglutamate" EXACT PSI-MI-short [] synonym: "L-glutamyl-5-poly(ADP-ribose)" EXACT PSI-MI-alternate [] synonym: "L-isoglutamyl-poly(ADP-ribose)" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0531 name: o-(adp-ribosyl)-serine def: "Residue modification.\nOBSOLETE remap to MOD:00242." [PMID:14755292, RESID:AA0237] synonym: "(S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic acid Formula" EXACT PSI-MI-alternate [] synonym: "adp-ribosylserine" EXACT PSI-MI-short [] synonym: "O-(ADP-ribosyl)-L-serine" EXACT PSI-MI-alternate [] synonym: "O3-(ADP-ribosyl)-L-serine" EXACT PSI-MI-alternate [] synonym: "O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-serine" EXACT PSI-MI-alternate [] synonym: "O3-alpha-D-ribofuranosyl-L-serine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0532 name: n4-(adp-ribosyl)-asparagine def: "Residue modification.\nOBSOLETE remap to MOD:00236." [PMID:14755292, RESID:AA0231] synonym: "(S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-4-oxobutanoic acid" EXACT PSI-MI-alternate [] synonym: "adpribosylasparagine" EXACT PSI-MI-short [] synonym: "N4-(ADP-ribosyl)-L-asparagine" EXACT PSI-MI-alternate [] synonym: "N4-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-asparagine" EXACT PSI-MI-alternate [] synonym: "N4-alpha-D-ribofuranosyl-L-asparagine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0533 name: glycosylated residue def: "Residue modification.\nOBSOLETE remap to MOD:00693." [PMID:14755292] is_obsolete: true [Term] id: MI:0534 name: glycosyl-cysteine def: "Residue modification.\nOBSOLETE remap to MOD:00131." [PMID:14755292, RESID:AA0122] synonym: "S-glycosyl-L-cysteine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0535 name: glycosyl-serine def: "Residue modification.\nOBSOLETE remap to MOD:00163." [PMID:14755292, RESID:AA0154] synonym: "O-glycosyl-L-serine" EXACT PSI-MI-alternate [] synonym: "O3-glycosyl-L-serine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0536 name: glycosyl-threonine def: "Residue modification.\nOBSOLETE remap to MOD:00164." [PMID:14755292, RESID:AA0155] synonym: "O-glycosyl-L-threonine" EXACT PSI-MI-alternate [] synonym: "O3-glycosyl-L-threonine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0537 name: omega-n-glycosyl-arginine def: "Residue modification.\nOBSOLETE remap to MOD:00332." [PMID:14755292, RESID:AA0327] synonym: "glycosylarginine" EXACT PSI-MI-short [] synonym: "omega-N-glycosyl-L-arginine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0538 name: n4-glycosyl-asparagine def: "Residue modification.\nOBSOLETE remap to MOD:00160." [PMID:14755292, RESID:AA0151] synonym: "glycosylasparagine" EXACT PSI-MI-short [] synonym: "N4-glycosyl-L-asparagine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0539 name: gpi anchor residue def: "Residue modification.\nOBSOLETE remap to MOD:00818." [PMID:14755292] is_obsolete: true [Term] id: MI:0540 name: gpi-anchor amidated alanine def: "Residue modification.\nOBSOLETE remap to MOD:00172." [PMID:14755292, RESID:AA0163] synonym: "gpi-alanine" EXACT PSI-MI-short [] synonym: "N-alanyl-glycosylphosphatidylinositolethanolamine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0541 name: gpi-anchor amidated asparagine def: "Residue modification.\nOBSOLETE remap to MOD:00167." [PMID:14755292, RESID:AA0158] synonym: "gpi-asparagine" EXACT PSI-MI-short [] synonym: "N-asparaginyl-glycosylphosphatidylinositolethanolamine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0542 name: gpi-anchor amidated aspartate def: "Residue modification.\nOBSOLETE remap to MOD:00168." [PMID:14755292, RESID:AA0159] synonym: "gpi-aspartate" EXACT PSI-MI-short [] synonym: "N-aspartyl-glycosylphosphatidylinositolethanolamine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0543 name: gpi-anchor amidated cysteine def: "Residue modification.\nOBSOLETE remap to MOD:00169." [PMID:14755292, RESID:AA0160] synonym: "gpi-cysteine" EXACT PSI-MI-short [] synonym: "N-cysteinyl-glycosylphosphatidylinositolethanolamine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0544 name: gpi-anchor amidated glycine def: "Residue modification.\nOBSOLETE remap to MOD:00170." [PMID:14755292, RESID:AA0161] synonym: "gpi-glycine" EXACT PSI-MI-short [] synonym: "N-glycyl-glycosylphosphatidylinositolethanolamine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0545 name: gpi-anchor amidated serine def: "Residue modification.\nOBSOLETE remap to MOD:00171." [PMID:14755292, RESID:AA0162] synonym: "gpi-serine" EXACT PSI-MI-short [] synonym: "N-seryl-glycosylphosphatidylinositolethanolamine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0546 name: gpi-anchor amidated threonine def: "Residue modification.\nOBSOLETE remap to MOD:00173." [PMID:14755292, RESID:AA0164] synonym: "gpi-threonine" EXACT PSI-MI-short [] synonym: "N-threonyl-glycosylphosphatidylinositolethanolamine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0547 name: s-prenyl-cysteine def: "Residue modification.\nOBSOLETE remap to MOD:01110." [PMID:14755292] synonym: "prenylcysteine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0548 name: methylated-lysine def: "Residue modification.\nOBSOLETE remap to MOD:00663." [PMID:14755292, RESID:AA0074, RESID:AA0075, RESID:AA0076] synonym: "methylatedlysine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0549 name: alkylated cysteine def: "Artificial residue modification enabling studies of cysteine binding status.\nOBSOLETE remap to MOD:00660." [PMID:15325307] is_obsolete: true [Term] id: MI:0550 name: gamma-carboxyglutamic acid def: "Residue modification.\nOBSOLETE remap to MOD:00041." [PMID:14755292, RESID:AA0032] synonym: "(S)-3-amino-1,1,3-propanetricarboxylic acid" EXACT PSI-MI-alternate [] synonym: "1-carboxyglutamic acid [misnomer]" EXACT PSI-MI-alternate [] synonym: "4-carboxyglutamic acid" EXACT PSI-MI-alternate [] synonym: "carboxyglutamic acid" EXACT PSI-MI-short [] synonym: "L-gamma-carboxyglutamic acid" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0551 name: nitro-tyrosine def: "Residue modification.\nOBSOLETE remap to MOD:00461." [PMID:15657065, PMID:9636206] synonym: "nitrated tyrosine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0552 name: s-nitrosyl-cysteine def: "Residue modification.\nOBSOLETE remap to MOD:00235." [PMID:14755292, RESID:AA0230] synonym: "(R)-2-amino-3-nitrososulfanyl-propanoic acid" EXACT PSI-MI-alternate [] synonym: "L-cysteine nitrite ester" EXACT PSI-MI-alternate [] synonym: "nitrosylcysteine" EXACT PSI-MI-short [] synonym: "S-nitrosocysteine" EXACT PSI-MI-alternate [] synonym: "S-nitrosyl-L-cysteine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0553 name: o4'-sulfo-tyrosine def: "Residue modification.\nOBSOLETE remap to MOD:00181." [PMID:14755292, RESID:AA0172] synonym: "(S)-2-amino-3-(4-sulfooxyphenyl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-sulfate" EXACT PSI-MI-alternate [] synonym: "O4'-sulfo-L-tyrosine" EXACT PSI-MI-alternate [] synonym: "O4-sulfotyrosine" EXACT PSI-MI-alternate [] synonym: "sulfotyrosine" EXACT PSI-MI-short [] synonym: "tyrosine sulfate" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0554 name: sumoylated lysine def: "Residue modification due to a cross-link between a lysine and a glycine from the sumo (Small Ubiquitin-related MOdifier) protein.\nOBSOLETE remap to MOD:01149." [PMID:12612601, RESID:AA0125] synonym: "(S)-2-amino-6-[(aminoacetyl)amino]hexanoic acid" EXACT PSI-MI-alternate [] synonym: "N6-glycyl-L-lysine" EXACT PSI-MI-alternate [] synonym: "N6-glycyllysine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0555 name: phospho-histidine def: "Residue modification.\nOBSOLETE remap to MOD:00890." [PMID:14755292, RESID:AA0035, RESID:AA0036] synonym: "phosphoshistidine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0556 name: transglutamination reaction def: "Gln-Lys cross-link catalyzed by a transglutaminase." [PMID:14755292, RESID:AA0124] subset: PSI-MI_slim synonym: "transglutamination" EXACT PSI-MI-short [] is_a: MI:0195 ! covalent binding [Term] id: MI:0557 name: adp ribosylation reaction def: "Involves the addition of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues." [GO:0006471, PMID:14755292, RESID:AA0168, RESID:AA0169, RESID:AA0231, RESID:AA0237, RESID:AA0295] subset: PSI-MI_slim synonym: "adp ribosylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0558 name: deglycosylation reaction def: "Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins." [GO:0006517, PMID:15670854] subset: PSI-MI_slim synonym: "deglycosylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0559 name: glycosylation reaction def: "The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Reaction that can affect Ser, Thr, Cys, Arg, and Asn residues. This reaction is known to be reversible in the case of Asn substrate." [GO:0043413, PMID:14755292, RESID:AA0122, RESID:AA0151, RESID:AA0154, RESID:AA0155, RESID:AA0327] subset: PSI-MI_slim synonym: "glycosylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0560 name: myristoylated residue def: "Residue modification.\nOBSOLETE remap to MOD:00438." [PMID:14755292] synonym: "myristoylated aa" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0561 name: palmitoylated residue def: "Residue modification.\nOBSOLETE remap to MOD:00440." [PMID:14755292] synonym: "palmitoylated aa" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0562 name: methylated alanine def: "Residue modification.\nOBSOLETE remap to MOD:00665." [PMID:14755292, RESID:AA0061, RESID:AA0062] is_obsolete: true [Term] id: MI:0563 name: methylated arginine def: "Residue modification.\nOBSOLETE remap to MOD:00658." [PMID:14755292, RESID:AA0068, RESID:AA0069] is_obsolete: true [Term] id: MI:0564 name: omega-n-methyl-arginine def: "Residue modification.\nOBSOLETE remap to MOD:00078." [PMID:14755292, RESID:AA0069] synonym: "(S)-2-amino-5-[(imino(methylamino)methyl)amino]pentanoic acid" EXACT PSI-MI-alternate [] synonym: "methylarginine" EXACT PSI-MI-short [] synonym: "NG-methylarginine;" EXACT PSI-MI-alternate [] synonym: "omega-N-methyl-L-arginine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0565 name: neddylated lysine def: "Residue modification due to a cross-link between a lysine and a glycine from the Nedd8 protein family.\nOBSOLETE remap to MOD:01150." [PMID:111] is_obsolete: true [Term] id: MI:0566 name: sumoylation reaction def: "Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target." [GO:0016925, PMID:15985640] subset: PSI-MI_slim synonym: "sumoylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0567 name: neddylation reaction def: "Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target." [GO:0045116, PMID:16127432] subset: PSI-MI_slim synonym: "neddylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0568 name: desumoylation reaction def: "Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins." [GO:0016926, PMID:15985640] subset: PSI-MI_slim synonym: "desumoylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0569 name: deneddylation reaction def: "Cleavage of the G-K bond and release of the NEDD8 ubiquitin like proteins. Deneddylation, which removes the NEDD8 moiety, requires the isopeptidase activity of the COP9 signalosome." [GO:0000338, PMID:16127432] subset: PSI-MI_slim synonym: "deneddylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0570 name: protein cleavage def: "Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation." [PMID:14744292] subset: PSI-MI_slim is_a: MI:0194 ! cleavage reaction [Term] id: MI:0571 name: mrna cleavage def: "Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner." [GO:0006379, PMID:14681407] subset: PSI-MI_slim is_a: MI:0902 ! rna cleavage [Term] id: MI:0572 name: dna cleavage def: "Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0910 ! nucleic acid cleavage [Term] id: MI:0573 name: mutation disrupting interaction def: "Region of a molecule whose mutation or deletion totally disrupts an interaction strength or rate (in the case of interactions inferred from enzymatic reaction).." [PMID:14755292] subset: PSI-MI_slim synonym: "mutation disrupting" EXACT PSI-MI-short [] is_a: MI:0119 ! mutation decreasing interaction [Term] id: MI:0574 name: digital object identifier def: "Identifier of a publication prior to pubmed indexing." [PMID:14755292] subset: PSI-MI_slim synonym: "doi" EXACT PSI-MI-short [] xref: id-validation-regexp: "\\d+.\\d+/[a-zA-Z0-9\\.\\:]+" xref: search-url: "http://dx.doi.org/${ac}" is_a: MI:0445 ! literature database [Term] id: MI:0575 name: alliance for cellular signaling def: "Alliance for Cellular Signaling (AfCS -Nature) store yeast 2-hybrid Interaction data and expression data. Information and data are freely available to all.\nhttp://www.signaling-gateway.org" [PMID:14755292] subset: PSI-MI_slim synonym: "AfCS" EXACT PSI-MI-alternate [] synonym: "afcs" EXACT PSI-MI-short [] xref: id-validation-regexp: "[0-9]+" xref: search-url: "http://www.signaling-gateway.org/data/Y2H/cgi-bin/y2h_int.cgi?id=${ac}" is_a: MI:0461 ! interaction database is_a: MI:0489 ! source database [Term] id: MI:0576 name: structural proximity def: "Method to identify domain-domain interactions within the same resolved structure. Domains are first projected onto a pdb structure and then the distance between all pairs of residues in different domains are calculated. When the distance between 2 residues is below the non covalent bond threshold, the corresponding pair of domains is predicted to interact." [PMID:15353450] subset: PSI-MI_slim is_a: MI:0577 ! feature prediction from structure [Term] id: MI:0577 name: feature prediction from structure def: "Group of method taking advantage of 3D structure to calculate and infer the feature of interacting molecules." [PMID:14755292] subset: PSI-MI_slim synonym: "feature struct pred" EXACT PSI-MI-short [] is_a: MI:0660 ! feature prediction [Term] id: MI:0578 name: maltose binding protein tag def: "The protein is expressed and purified as a fusion to the glutathione maltose-binding protein (MBP). The MBP-fusion protein can be purified by affinity chromatography using an amylose resin." [PMID:14755292] subset: PSI-MI_slim synonym: "maltose binding protein tag" EXACT PSI-MI-alternate [] synonym: "mbp tag" EXACT PSI-MI-short [] is_a: MI:0240 ! fusion protein [Term] id: MI:0579 name: electron donor def: "Any molecule that is able to transfer an electron to another chemical species." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0918 ! donor [Term] id: MI:0580 name: electron acceptor def: "Molecule to which an electron may be transferred from an electron donor." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0919 ! acceptor [Term] id: MI:0581 name: suppressor gene def: "Gene whose mutation suppress the phenotype associated to a suppressed mutation." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role [Term] id: MI:0582 name: suppressed gene def: "Gene whose mutation phenotype is suppressed by a given suppressor mutation." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role [Term] id: MI:0583 name: fluorescence donor def: "Fluorophore which emits electromagnetic radiation of given wavelength." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role [Term] id: MI:0584 name: fluorescence acceptor def: "Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific donor fluorophore, the re-emission of its own characteristic fluorescence." [PMID:14755292] subset: PSI-MI_slim synonym: "fluorescence accept" EXACT PSI-MI-short [] is_a: MI:0495 ! experimental role [Term] id: MI:0585 name: intenz def: "IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at.\nhttp://www.ebi.ac.uk/intenz" [PMID:14681451] subset: PSI-MI_slim xref: id-validation-regexp: "[0-6]{1}\\.(\\d+|-)\\.(\\d+|-)\\.(\\d+|-)" xref: search-url: "http://www.ebi.ac.uk/intenz/query?cmd=Search&q=${ac}&t=exact&fields=ec" is_a: MI:0461 ! interaction database [Term] id: MI:0586 name: inhibitor def: "Molecule inhibiting an interaction by interacting with one or more of its participants." [PMID:14755292] subset: PSI-MI_slim is_a: MI:2274 ! regulator [Term] id: MI:0587 name: inhibited def: "Molecule being identified as target of an inhibitor.\nOBSOLETE as term is deprecated to describe the target of an inhibitor that can have any other biological role." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0588 name: three hybrid def: "Group of methods based on complementation assay where a third participant is shown to be necessary for the binding of a given bait prey pair. The molecule fused to the DNA binding domain is the bait, that fused to the transcriptional activator is the prey." [PMID:14755292] subset: PSI-MI_slim synonym: "3 hybrid" EXACT PSI-MI-short [] synonym: "3-hybrid" EXACT PSI-MI-alternate [] synonym: "tri hybrid" EXACT PSI-MI-alternate [] synonym: "tri-hybrid assay" EXACT PSI-MI-alternate [] is_a: MI:0232 ! transcriptional complementation assay [Term] id: MI:0589 name: in vitro translated protein def: "Protein sample collected by in vitro translation of its mRNA taking advantage of purified translation machinery." [PMID:14755292] subset: PSI-MI_slim synonym: "in vitro translated" EXACT PSI-MI-short [] is_a: MI:0342 ! sample process [Term] id: MI:0590 name: attribute name def: "Collection of topics describing the free text stored as an attribute value." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "CvTopic" EXACT PSI-MI-alternate [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0591 name: experiment description def: "The experimental condition text description, should contain information about the organisms hosting the interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "experiment descripti" EXACT PSI-MI-short [] is_a: MI:0665 ! experiment attribute name [Term] id: MI:0592 name: ipfam def: "Web resource that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues. iPfam is available on the Web for browsing at.\nhttp://www.sanger.ac.uk/Software/Pfam/iPfam/" [PMID:15353450] subset: PSI-MI_slim is_a: MI:0447 ! feature database [Term] id: MI:0593 name: translocation def: "Xref pointing to a GO process term describing the start and end location of a migrating molecule, for instance see GO:0006611, 'protein-nucleus export'." [PMID:14681407] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0594 name: translocation start def: "Xref pointing to a GO compartment term describing the start location of a migrating molecule." [PMID:14681407] subset: PSI-MI_slim is_a: MI:0593 ! translocation [Term] id: MI:0595 name: translocation end def: "Xref pointing to a GO compartment term describing the end location of a migrating molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0593 ! translocation [Term] id: MI:0596 name: experimental form description def: "Free text description of all the tags and artificial process undergone by a molecule during an experiment." [PMID:14755292] subset: PSI-MI_slim synonym: "experimental form de" EXACT PSI-MI-short [] is_a: MI:0666 ! participant attribute name [Term] id: MI:0597 name: feature description def: "The feature text description may include information about the feature detection method." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0668 ! feature attribute name [Term] id: MI:0598 name: feature constraint def: "The feature constraint free text will specificity whether a biological feature is shown to be possible (just observed) or required (experimentally demonstrated to be necessary for an interaction)." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0668 ! feature attribute name [Term] id: MI:0599 name: figure legend def: "Text pointing to a specific paper figure legend where the experimental evidences for an interaction are to be found." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:0665 ! experiment attribute name [Term] id: MI:0600 name: conditional synthetic lethal nutrition-sensitivity def: "Two silent mutations show a nutrition sensitive lethal phenotype when they co-occur on the same cell.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description." [PMID:15608217] subset: PSI-MI_slim synonym: "nutrition synt letal" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0601 name: sequence ontology def: "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data." [PMID:15892872] subset: PSI-MI_slim synonym: "so" EXACT PSI-MI-short [] xref: id-validation-regexp: "SO:[0-9]{7}" is_a: MI:0447 ! feature database is_a: MI:0473 ! participant database [Term] id: MI:0602 name: chemical footprinting def: "Binding sites are identified by altered reactivity of a complex to a chemical treatment compared to the unbound molecules. Residues in close contact with the binding partner are protected from chemical modification. When these chemicals are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo." [PMID:8238889] subset: PSI-MI_slim synonym: "chemical footprint" EXACT PSI-MI-short [] is_a: MI:0417 ! footprinting [Term] id: MI:0603 name: dimethylsulphate footprinting def: "Dimethylsulphate (DMS) is the most commonly used chemical to study DNA-protein interactions. DMS induces methylation of guanine residues so DNA interaction with protein binding to AT rich sequences or to the phosphate backbone may be not detected by DMS footprinting. However as DMS diffuses across membrane it can also be used for in vivo footprinting. The experiment involves the treatment with DMS of two DNA samples with identical sequence, one protein bound and the other naked. The two samples are treated with piperidine to induce chemical cleavage of the DMS modified guanine residues followed by digestion with restriction enzymes. Once labelled the samples are run in parallel on a gel to visualize the pattern of nested fragments sharing a common end generated by restriction enzyme(or PCR primer extension) and a variable end guanine dependent. The missing bands of the protein bound sample correspond to the guanine residues protected from modification by an interaction." [PMID:8238889] subset: PSI-MI_slim synonym: "dms footprinting" EXACT PSI-MI-short [] is_a: MI:0602 ! chemical footprinting [Term] id: MI:0604 name: potassium permanganate footprinting def: "Potassium permanganate bind to single-stranded pyrimidine residues, it is commonly used to detect promoters opening regions in vivo. KMnO4 treatment of cells, followed by treatment with piperidine, followed by either PCR and/or acrylamide gel electrophoresis allows detection of interaction between transcription factor and the DNA sequence under their control." [PMID:8238889] subset: PSI-MI_slim synonym: "k-mn-04 footprinting" EXACT PSI-MI-short [] is_a: MI:0602 ! chemical footprinting [Term] id: MI:0605 name: enzymatic footprinting def: "Binding sites are identified by altered reactivity of a complex to an enzymatic probe compared to the unbound molecules. Residues in close contact with the binding partner are protected from cleavage by the enzyme. When these enzymes are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo." [PMID:8238889] subset: PSI-MI_slim synonym: "enzymatic footprint" EXACT PSI-MI-short [] is_a: MI:0417 ! footprinting [Term] id: MI:0606 name: DNase I footprinting def: "Deoxyribonuclease I (DNase I) does not have high specificity for given sequences or residues, thus footprinting with DNase I permits the exact delineation of the protein-DNA binding site. Moreover DNase I, can be used for in vivo footprinting by treating intact cells with permeabilising drugs. In this latter case DNase I in vivo footprinting allow studies of the chromatin structure in genomic DNA." [PMID:8238889] subset: PSI-MI_slim synonym: "dnase 1 footprinting" EXACT PSI-MI-short [] synonym: "DNase I protection" RELATED [] is_a: MI:1183 ! nuclease footprinting [Term] id: MI:0607 name: small nuclear rna def: "These RNA molecules are relatively short (less than 200 nucleotides each), and there are five of them (U1, U2, U4, U5, and U6) involved in the major form of pre-mRNA splicing. Known as snRNAs (small nuclear RNAs), each is complexed with at least seven protein subunits to form a snRNP (small nuclear ribonucleoprotein). These snRNPs form the core of the spliceosome." [PMID:14755292] subset: PSI-MI_slim synonym: "snRNA" EXACT PSI-MI-alternate [] synonym: "snrna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0608 name: ribosomal rna def: "RNA that is transcribed from the DNA of the nucleolus and is found, together with characteristic proteins, in the ribosomes." [PMID:14755292] subset: PSI-MI_slim synonym: "rRNA" EXACT PSI-MI-alternate [] synonym: "rrna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0609 name: small nucleolar rna def: "The small nucleolar RNAs, are stable RNA contained in the nucleoli and these RNAs exist as snoRNA: protein complexes called snoRNPs (also called 'snorps'). The snoRNPs function is in the maturation of ribosomal RNA and other RNAs, by: creating two types of modified nucleotides, (2'-O-methylated nucleotides and pseudouridine), and mediating endonucleolytic cleavages of pre-rRNA." [PMID:14755292] subset: PSI-MI_slim synonym: "snoRNA" EXACT PSI-MI-alternate [] synonym: "snorna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0610 name: small interfering rna def: "Ribonucleic acid used in RNAi study. These RNA have the reverse complementary sequence of a target gene's mRNA transcript and inhibit its expression." [PMID:10542148] subset: PSI-MI_slim synonym: "dicer RNA" EXACT PSI-MI-alternate [] synonym: "micro RNA" EXACT PSI-MI-alternate [] synonym: "siRNA" EXACT PSI-MI-alternate [] synonym: "sirna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0611 name: signal recognition particle rna def: "Small (300 nucleotides) stable RNAs transcribed by RNA pol III that are part of the signal-recognition particle (SRP). This particle comprises one RNA and six proteins bound to the RNA. SRP function is to assist secretory proteins sorting in the endoplasmic reticulum (ER). SRP is a cytosolic particle that transiently binds to the ER signal sequence of a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane." [PMID:14755292] subset: PSI-MI_slim synonym: "srpRNA" EXACT PSI-MI-alternate [] synonym: "srprna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0612 name: comment def: "Comment for public view. This attribute can be associated to interaction, experiment, CV term, an organism and any participant." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:0665 ! experiment attribute name is_a: MI:0666 ! participant attribute name is_a: MI:0667 ! controlled vocabulary attribute name is_a: MI:0668 ! feature attribute name is_a: MI:0669 ! organism attribute name [Term] id: MI:0613 name: function def: "Biological function of a participant or of an interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:0666 ! participant attribute name [Term] id: MI:0614 name: url def: "URL/Web address describing an experiment, an interaction, a Cv term or an organism." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:0665 ! experiment attribute name is_a: MI:0667 ! controlled vocabulary attribute name is_a: MI:0669 ! organism attribute name [Term] id: MI:0615 name: search-url def: "Search engine URL associated to Cv Database terms." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0667 ! controlled vocabulary attribute name [Term] id: MI:0616 name: example def: "Example generally associated to Cv terms. Test." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0667 ! controlled vocabulary attribute name is_a: MI:1041 ! synonym [Term] id: MI:0617 name: disease def: "The interaction has a known or demonstrated disease association." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0618 name: caution def: "Warning about errors or grounds for confusion. Can be associated to an interaction, experiment, CV term or any participant." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:0665 ! experiment attribute name is_a: MI:0666 ! participant attribute name is_a: MI:0667 ! controlled vocabulary attribute name is_a: MI:0668 ! feature attribute name is_a: MI:0669 ! organism attribute name [Term] id: MI:0619 name: pathway def: "Refers to the metabolic or signalling pathway involving an interaction or a complex." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0620 name: search-url-ascii def: "Search URL to retrieve an external entry in ASCII format. Generally associated to Cv Database terms." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0667 ! controlled vocabulary attribute name [Term] id: MI:0621 name: author-confidence def: "Confidence classification assigned by the author of the publication to a specific interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0622 name: confidence-mapping def: "Description of confidence assessment method generally associated to the experiment." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0665 ! experiment attribute name [Term] id: MI:0623 name: inhibition def: "The interaction between the proteins or the formation of a complex is disrupted by a biological molecule or by a modification of the interactors." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0624 name: stimulant def: "Reaction occurs at a faster rate in the presence of this compound or molecule i.e. the molecule directly physically co-operates with the interaction. Reaction may not occur at all in the absence of this molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0625 name: agonist def: "Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that stimulates an interaction, potentially by causing modification of one or more of the interactors." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0626 name: antagonist def: "Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that inhibits an interaction, potentially by alteration of amount or binding affinity of one or more of the interactors." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0627 name: experiment modification def: "Modifications of the standard experimental method described in the CV." [PMID:14755292] subset: PSI-MI_slim synonym: "exp-modification" EXACT PSI-MI-short [] is_a: MI:0665 ! experiment attribute name [Term] id: MI:0628 name: validation regular expression def: "Regular Expression used to check the validity of cross references' identifier. Attribute generally associated to terms in Cv Database." [PMID:14755292] subset: PSI-MI_slim synonym: "id-validation-regexp" EXACT PSI-MI-short [] is_a: MI:0667 ! controlled vocabulary attribute name [Term] id: MI:0629 name: complex-properties def: "Information on the complex being annotated. Attribute generally associated to an interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:0665 ! experiment attribute name [Term] id: MI:0630 name: 3d-structure def: "Comments on the 3D structure. This attribute is generally associated to an interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0631 name: 3d-r-factors def: "Free R-Factor and working R-Factor for the quality of the crystallographic model. This attribute is generally associated to an interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0632 name: 3d-resolution def: "Resolution of the 3D structure. This attribute is generally associated to an interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0633 name: data-processing def: "Information about how the data was processed. This attribute is used mainly for large scale experiment." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0665 ! experiment attribute name [Term] id: MI:0634 name: contact-email def: "E-mail address to contact the author or organisation which has produced the data. This attribute is generally associated to an experiment." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1093 ! bibliographic attribute name [Term] id: MI:0635 name: contact-comment def: "Free text notes on how to contact the author or organisation which has produced the data This attribute is generally associated to an experiment." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1093 ! bibliographic attribute name [Term] id: MI:0636 name: author-list def: "List of authors associated to a publication. This attribute is generally associated to an experiment." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1093 ! bibliographic attribute name [Term] id: MI:0637 name: isoform-comment def: "Participant isoform's comment. This attribute can be attached to interactions or participants." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:0666 ! participant attribute name [Term] id: MI:0638 name: prerequisite-ptm def: "Post translational modification required for an interaction to occur." [PMID:14755292] subset: PSI-MI_slim synonym: "prerequisite ptm" EXACT PSI-MI-alternate [] synonym: "prerequisite-ptm" EXACT PSI-MI-short [] synonym: "required ptm" EXACT PSI-MI-alternate [] synonym: "required-ptm" EXACT PSI-MI-alternate [] is_a: MI:0925 ! observed-ptm [Term] id: MI:0639 name: resulting-ptm def: "Post translational modification occurs subsequently to an interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "resulting ptm" EXACT PSI-MI-alternate [] synonym: "resulting-ptm" EXACT PSI-MI-short [] is_a: MI:0925 ! observed-ptm [Term] id: MI:0640 name: parameter type def: "Parameter for enzymatic or binding kinetic studies." [PMID:14755292] subset: Drugable subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0641 name: ic50 def: "Molar concentration of an antagonist which produces 50% of the maximum possible inhibitory response for that antagonist. Note this measure depends on the specific antagonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ic50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar." [PMID:14755292] subset: PSI-MI_slim synonym: "IC50" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:0642 name: ec50 def: "Molar concentration of an agonist which produces 50% of the maximum possible response for that agonist. Note this measure depends on the specific agonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ec50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar." [PMID:14755292] subset: PSI-MI_slim synonym: "EC50" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:0643 name: ki def: "Equilibrium constant for dissociation of an inhibitor. Unit Molar." [PMID:14755292] subset: PSI-MI_slim synonym: "Ki" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:0644 name: km def: "Michaelis-Menten constant: concentration of substrate at which the reaction rate is equal to half the maximal rate (i.e. Km={s} when Vo=1/2Vmax). Unit Molar." [PMID:14755292] subset: PSI-MI_slim synonym: "Km" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:0645 name: kcat def: "The number of substrate molecules converted to product in a given unit of time, on a single enzyme molecule when the enzyme is saturated with substrate. Unit per second, or s-1." [PMID:14755292] subset: PSI-MI_slim synonym: "turnover number" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:0646 name: Kd def: "The equilibrium dissociation constant of a receptor/ligand or proteinA/proteinB complex. Unit Molar (generally M-1)." [PMID:14755292] subset: PSI-MI_slim synonym: "Kd" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:0647 name: parameter unit def: "Controlled vocabulary for kinetic constant units." [PMID:14755292] subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0648 name: molar def: "Molarity is the number of moles of solute dissolved in one liter of solution. The units, therefore are moles per liter, specifically it's moles of solute per liter of solution. These units are abbreviated as M and it means moles per liter (not just moles)." [PMID:14755292] subset: PSI-MI_slim synonym: "M" EXACT PSI-MI-alternate [] is_a: MI:0647 ! parameter unit [Term] id: MI:0649 name: second def: "The second is the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the cesium-133 atom. The second was originally defined as 1/86 400 mean solar day until astronomers discovered that the mean solar day is actually not constant." [PMID:14755292] subset: PSI-MI_slim synonym: "s" EXACT PSI-MI-alternate [] synonym: "sec" EXACT PSI-MI-alternate [] is_a: MI:0647 ! parameter unit [Term] id: MI:0650 name: millimolar def: "10E-3 moles per liter of solution.\nOBSOLETE: term redundant with the schema exponent attribute of the parameter." [PMID:14755292] subset: PSI-MI_slim synonym: "mM" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0651 name: micromolar def: "10E-6 moles per liter of solution.\nOBSOLETE: term redundant with the schema exponent attribute of the parameter." [PMID:14755292] subset: PSI-MI_slim synonym: "uM" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0652 name: nanomolar def: "10E-9 moles per liter of solution.\nOBSOLETE: term redundant with the schema exponent attribute of the parameter." [PMID:14755292] subset: PSI-MI_slim synonym: "nM" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0653 name: picomolar def: "10E-12 moles per liter of solution.\nOBSOLETE: term redundant with the schema exponent attribute of the parameter." [PMID:14755292] subset: PSI-MI_slim synonym: "pM" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0654 name: fentomolar def: "10E-15 moles per liter of solution.\nOBSOLETE: term redundant with the schema exponent attribute of the parameter." [PMID:14755292] subset: PSI-MI_slim synonym: "fM" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0655 name: lambda repressor two hybrid def: "A protein of interest (the bait) is fused to the full-length bacteriophage lambda repressor protein (lambdacI, 237 amino acids), containing the amino terminal DNA-binding domain and the carboxylterminal dimerization domain. The corresponding target (prey) protein is fused to the N-terminal domain of the alfa-subunit of RNA polymerase (248 amino acids). The bait is tethered to the lambda operator sequence upstream of the reporter promoter through the DNA-binding domain of lambdacI. When the bait and prey interact, they recruit and stabilize the binding of RNA polymerase at the promoter and activate the transcription of the HIS3 reporter gene. Due to the tendency of both the lambda repressor protein and the N-terminal domain of the alfa-subunit of RNA polymerase to dimerize, this system might not be optimal for the analysis of proteins that self-associate unless their interaction with other protein partners depends on the oligomerization." [PMID:15792953] subset: PSI-MI_slim synonym: "BacterioMatch" EXACT PSI-MI-alternate [] synonym: "lambda two hybrid" EXACT PSI-MI-short [] is_a: MI:0232 ! transcriptional complementation assay [Term] id: MI:0656 name: identified peptide def: "Peptide whose sequence is experimentally identified and can lead to a full protein identification." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0505 ! experimental feature [Term] id: MI:0657 name: systematic evolution of ligands by exponential enrichment def: "RNA and cDNA constructs with variable central sequences and a constant flanking region are collected in a complex library. The library is then screened to select either specific binding partners of a bait molecule (generally a protein) or particular enzymatic activities of the nucleic acid molecules themselves. The selected nucleic acids are amplified using the constant flanking regions to increase their abundance. Cycles of selection-amplification can be repeated to increase the specificity of the targets that, at the end, are individually identified by sequencing." [PMID:11539574] subset: PSI-MI_slim synonym: "in vitro evolution of nucleic acids" EXACT PSI-MI-alternate [] synonym: "selex" EXACT PSI-MI-short [] is_a: MI:0400 ! affinity technology [Term] id: MI:0658 name: multidimensional protein identification technology def: "MudPIT is a method for rapid and large-scale protein identification by multidimensional liquid chromatography associated with tandem mass spectrometry. The chromatography step consists of strong cation exchange material back-to-back with reversed phase material inside fused silica capillaries. The peptides bound to the cation-exchange resin are freed by the gradually increasing salt concentration of the buffer and are subsequently retained by the reversed phase resin. Increasing buffers hydrophobicity progressively elute peptides from the reversed phase packing directly into the mass spectrometer. Typically this mass spectrometer will be a tandem electrospray, so peptides undergo ionization in the liquid phase, are separated in a primary mass spectrometer, analysed in the second mass spectrometer and identified." [PMID:11231557] subset: PSI-MI_slim synonym: "mudpit" EXACT PSI-MI-short [] is_a: MI:0093 ! protein sequence identification is_a: MI:0427 ! Identification by mass spectrometry is_a: MI:0815 ! confirmation by molecular weight [Term] id: MI:0659 name: experimental feature detection def: "Experimental method by which a feature is detected or identified." [PMID:14755292] subset: PSI-MI_slim synonym: "exp feature detect" EXACT PSI-MI-short [] is_a: MI:0003 ! feature detection method [Term] id: MI:0660 name: feature prediction def: "Feature detection based on computational analysis." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0003 ! feature detection method [Term] id: MI:0661 name: experimental participant identification def: "experimental participant identification." [PMID:14755292] subset: PSI-MI_slim synonym: "experimental particp" EXACT PSI-MI-short [] is_a: MI:0002 ! participant identification method [Term] id: MI:0662 name: imex-primary def: "IMEx primary identifier that is assigned to an experiment record by the database that created the record in the context of IMEx consortium. The identifiers are unique across all member database as they are all generated by a centralized key-assigner.\nhttp://imex.sourceforge.net/" [PMID:14755292] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0663 name: confocal microscopy def: "A confocal is a standard epifluorescence microscope with improvement essentially coming from the rejection of out-of-focus light interference. Confocal imaging system achieves this by two strategies: a) by illuminating a single point of the specimen at any one time with a focused beam, so that illumination intensity drops off rapidly and b) by the use of blocking a pinhole aperture in a conjugate focal plane to the specimen so that light emitted away from the point in the specimen being illuminated is blocked from reaching the detector. Only the light from the single point illuminated of the specimen passing through the image pinhole is detected by a photodetector. Usually a computer is used to control the sequential scanning of the sample and to assemble the image for display onto a video screen." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0428 ! imaging technique [Term] id: MI:0664 name: interaction attribute name def: "Attribute name of annotation associated to an interaction element." [PMID:14755292] subset: PSI-MI_slim synonym: "interaction att name" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:0665 name: experiment attribute name def: "Attribute name of annotation associated to an experiment element." [PMID:14755292] subset: PSI-MI_slim synonym: "experiment att name" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:0666 name: participant attribute name def: "Attribute name of annotation associated to a participant element." [PMID:14755292] subset: PSI-MI_slim synonym: "participant att name" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:0667 name: controlled vocabulary attribute name def: "Attribute name of annotation associated to a CV term." [PMID:14755292] subset: PSI-MI_slim synonym: "cv att name" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:0668 name: feature attribute name def: "Attribute name of annotation associated to a feature element." [PMID:14755292] subset: PSI-MI_slim synonym: "feature att name" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:0669 name: organism attribute name def: "Attribute name of annotation associated to an organism element." [PMID:14755292] subset: PSI-MI_slim synonym: "organism att name" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:0670 name: imex def: "International Molecular Interaction Exchange." [PMID:22453911] subset: PSI-MI_slim synonym: "IMEx" EXACT PSI-MI-alternate [] xref: search-url: "http://www.ebi.ac.uk/intact/imex/main.xhtml?query=${ac}" is_a: MI:0461 ! interaction database [Term] id: MI:0671 name: antibodies def: "This annotation topic should contain information about antibodies when specific antibodies (monoclonal or polyclonal raised against specific regions of the proteins or purified in a specific manner) have been used." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0665 ! experiment attribute name [Term] id: MI:0672 name: library-used def: "This annotation topic will be used to store information about the cDNA library. If a name is available this should be reported along with a short description of the library." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0665 ! experiment attribute name [Term] id: MI:0673 name: complex synonym def: "Alternative names to describe a complex." [PMID:14755292] subset: PSI-MI_slim synonym: "complex-synonym" EXACT [] is_a: MI:1041 ! synonym [Term] id: MI:0674 name: peptide parent sequence reference def: "Describe a cross reference pointing to a peptide parent sequence." [PMID:14755292] subset: PSI-MI_slim synonym: "peptide-parent" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0675 name: international protein index def: "IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources." [PMID:15221759] subset: PSI-MI_slim synonym: "ipi" EXACT PSI-MI-short [] xref: id-validation-regexp: "IPI[0-9]+.[0-9]+|IPI[0-9]+" is_a: MI:1096 ! protein sequence databases [Term] id: MI:0676 name: tandem affinity purification def: "Tandem affinity purification allows rapid purification under native conditions of complexes, even when expressed at their natural level. Prior knowledge of complex composition or function is not required. The TAP method requires fusion of the a multiple tag, either N- or C-terminally, to the target (or bait) protein of interest. The multiple tag allows two steps purification steps ensuring a highly selective complex purification." [PMID:11403571] subset: PSI-MI_slim synonym: "TAP" EXACT PSI-MI-alternate [] synonym: "tap" EXACT PSI-MI-short [] is_a: MI:0004 ! affinity chromatography technology [Term] id: MI:0677 name: tandem tag def: "A tandem tag consists of the concatenation of simple distinct tags that is engineered to be cloned as a unique element onto a sequence of interest. Note that when a protein is fused to many simple tags that are inserted individually and possibly in different sequence positions these should be reported as independent features." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0507 ! tag [Term] id: MI:0678 name: antibody array def: "A microarray consisting of antibodies spotted on a solid support in appropriate orientation is incubated with a biological sample (or antigen). Some proteins are captured by the antibodies in the array. Protein of forming complexes on the array are identified according to their prior labelling (tag, ELISA, biotin and others)." [PMID:12454649] subset: PSI-MI_slim synonym: "antigen capture assay" EXACT PSI-MI-alternate [] synonym: "sandwich immunoassay" EXACT PSI-MI-alternate [] is_a: MI:0089 ! protein array [Term] id: MI:0679 name: poly adenine def: "A sequence of adenine nucleotides that is added to the 3' end of some primary transcript messenger RNA molecules in eukaryotes during post-transcriptional processing. The added tail is believed to confer stability to the molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "poly A" EXACT PSI-MI-alternate [] synonym: "poly a" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0680 name: single stranded deoxyribonucleic acid def: "DNA that consists of only one chain of nucleotides rather than the two base pairing strands found in DNA in the double helix form." [PMID:14755292] subset: PSI-MI_slim synonym: "ss DNA" EXACT PSI-MI-alternate [] synonym: "ss dna" EXACT PSI-MI-short [] is_a: MI:0319 ! deoxyribonucleic acid [Term] id: MI:0681 name: double stranded deoxyribonucleic acid def: "DNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides.\n" [PMID:14755292] subset: PSI-MI_slim synonym: "ds DNA" EXACT PSI-MI-alternate [] synonym: "ds dna" EXACT PSI-MI-short [] is_a: MI:0319 ! deoxyribonucleic acid [Term] id: MI:0682 name: cofactor def: "A cofactor is a small molecule required for the catalysis of an enzyme." [PMID:14755292] subset: PSI-MI_slim synonym: "coenzyme" EXACT PSI-MI-alternate [] is_a: MI:0500 ! biological role [Term] id: MI:0683 name: sequence database def: "Database collecting nucleic or amino acid sequences mainly derived from genomic or mRNA sequencing." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0473 ! participant database [Term] id: MI:0684 name: ancillary def: "Molecule required for an observed binary interaction to occur. This molecule may act as stabilizer of any of the interaction partners or may act as a bridge molecule between them but the method does not provide resolution or evidence to demonstrate its actual molecular function (i.e.Mudpit, tri hybrid etc)." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role is_a: MI:0500 ! biological role [Term] id: MI:0685 name: source reference def: "Publication or document describing the originating resource where an interaction, or other curated information, was first described." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0686 name: unspecified method def: "Yet to be identified interaction detection method associated with interaction data imported from a third party database. This database may have potentially different standards of curation." [PMID:14755292] subset: Drugable subset: PSI-MI_slim is_a: MI:0001 ! interaction detection method [Term] id: MI:0687 name: fluorescent protein tag def: "Protein having well characterized fluorescence excitation and emission spectra used as fusion with a protein under study to facilitate its localisation or identification." [PMID:14755292] subset: PSI-MI_slim synonym: "fluorescent prot tag" EXACT PSI-MI-short [] is_a: MI:0240 ! fusion protein [Term] id: MI:0688 name: dna binding domain tag def: "Part of a transcription factor responsible for the binding of gene regulatory region prior to their transcription. Such tags are generally used in two hybrid experiments where they are fused to a bait polypeptide tested for its ability to interact with a prey fused to an activation domain tag." [PMID:14755292] subset: PSI-MI_slim synonym: "dna binding domain" EXACT PSI-MI-short [] is_a: MI:0240 ! fusion protein [Term] id: MI:0689 name: activation domain tag def: "Part of a transcription factor responsible for the activation of DNA transcription. Such tags are generally used in two hybrid experiments where they are fused to a prey polypeptide tested for its ability to interact with a bait fused to a DNA binding domain tag." [PMID:14755292] subset: PSI-MI_slim synonym: "activation domain" EXACT PSI-MI-short [] is_a: MI:0240 ! fusion protein [Term] id: MI:0690 name: gal4 activation domain def: "Part of the yeast transcription factor GAL4 (amino acids 766-881) specifically responsible for DNA transcription activation." [PMID:14755292] subset: PSI-MI_slim synonym: "gal4 ad" EXACT PSI-MI-short [] is_a: MI:0689 ! activation domain tag [Term] id: MI:0691 name: vp16 activation domain def: "Full viral protein vp16 exclusively responsible for preferential transcriptional activation of viral genes. Activation requires the formation of a complex with the host cell transcription factor." [PMID:14755292] subset: PSI-MI_slim synonym: "vp16 ad" EXACT PSI-MI-short [] is_a: MI:0689 ! activation domain tag [Term] id: MI:0692 name: b42 activation domain def: "B42 is an acidic sequence of 89 residues derived from Escherichia coli acting as weak transcription activation domain. When use in two hybrid experiments, the weakness of B42 as activator increases the sensitivity of the interaction detection." [PMID:14613974] subset: PSI-MI_slim synonym: "b42 ad" EXACT PSI-MI-short [] is_a: MI:0689 ! activation domain tag [Term] id: MI:0693 name: gal4 dna binding domain def: "Part of the yeast transcription factor GAL4 (amino acids 11-38) specifically responsible for DNA binding of a 17 base-pair long sequence in the upstream activating sequence of galactose-induced genes.\n" [PMID:14755292] subset: PSI-MI_slim synonym: "gal4 dna bd" EXACT PSI-MI-short [] is_a: MI:0688 ! dna binding domain tag [Term] id: MI:0694 name: lexa dna binding domain def: "Amino terminal (1-220) part of the Escherichia coli lexA repressor, binding to 16 base pair palindromic DNA sequences." [PMID:14755292] subset: PSI-MI_slim synonym: "lexa dna bd" EXACT PSI-MI-short [] is_a: MI:0688 ! dna binding domain tag [Term] id: MI:0695 name: sandwich immunoassay def: "Antibody array where proteins retained by the arrayed antibodies are identified using a detector antibody. The detector antibody is either modified with a directly detectable label (enzyme, fluorescent molecule, isotope, etc.), or it is biotinylated for detection after subsequent probing with labeled streptavidin." [PMID:12454649] subset: PSI-MI_slim is_a: MI:0678 ! antibody array [Term] id: MI:0696 name: polymerase assay def: "Measures the catalysis of the transfer of a free nucleotidyl group to a nucleic acid chain." [PMID:14755292] subset: PSI-MI_slim synonym: "nucleotidyltransferase assay" EXACT PSI-MI-alternate [] is_a: MI:0415 ! enzymatic study [Term] id: MI:0697 name: dna directed dna polymerase assay def: "Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template or primer." [PMID:14755292] subset: PSI-MI_slim synonym: "dna dna pol assay" EXACT PSI-MI-short [] is_a: MI:0696 ! polymerase assay [Term] id: MI:0698 name: dna directed rna polymerase assay def: "Measures the catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [PMID:14755292] subset: PSI-MI_slim synonym: "dna rna pol assay" EXACT PSI-MI-short [] is_a: MI:0696 ! polymerase assay [Term] id: MI:0699 name: rna directed dna polymerase assay def: "Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time." [PMID:14755292] subset: PSI-MI_slim synonym: "rna dna pol assay" EXACT PSI-MI-short [] is_a: MI:0696 ! polymerase assay [Term] id: MI:0700 name: rna directed rna polymerase assay def: "Measures the catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template." [PMID:14755292] subset: PSI-MI_slim synonym: "rna rna pol assay" EXACT PSI-MI-short [] is_a: MI:0696 ! polymerase assay [Term] id: MI:0701 name: dna strand elongation def: "The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand." [GO:0006271, PMID:14755292] subset: PSI-MI_slim synonym: "dna elongation" EXACT PSI-MI-short [] synonym: "DNA replication elongation " EXACT PSI-MI-alternate [] is_a: MI:0986 ! nucleic acid strand elongation reaction [Term] id: MI:0702 name: panther def: "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.\nwww.pantherdb.org/" [PMID:14755292] subset: PSI-MI_slim synonym: "PANTHER" EXACT PSI-MI-alternate [] is_a: MI:0449 ! interpro [Term] id: MI:0703 name: gene3d def: "The Gene3D database provides a combined structural, functional and evolutionary view of the protein world. It is focused on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species.\nhttp://cathwww.biochem.ucl.ac.uk:8080/Gene3D/" [PMID:14755292] subset: PSI-MI_slim synonym: "Gene3D" EXACT PSI-MI-alternate [] is_a: MI:0449 ! interpro [Term] id: MI:0704 name: nucleic acid delivery def: "Method by which nucleic acids are delivered or engineered into a cell." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl delivery" EXACT PSI-MI-short [] is_a: MI:0307 ! delivery method [Term] id: MI:0705 name: anti tag western blot def: "Western blot assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag for which efficient antibodies are available. The antibody may be either monoclonal or polyclonal." [PMID:14755292] subset: PSI-MI_slim synonym: "anti tag western" EXACT PSI-MI-short [] is_a: MI:0113 ! western blot is_a: MI:0866 ! tag visualisation [Term] id: MI:0706 name: nucleic acid transformation def: "Transformation is the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material incorporated into the cell's genome (DNA or RNA)." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl transformation" EXACT PSI-MI-short [] is_a: MI:0704 ! nucleic acid delivery [Term] id: MI:0707 name: anti tag immunostaining def: "Immunostaining assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient antibodies are available. The anti tag antibody may be either monoclonal or polyclonal." [PMID:14755292] subset: PSI-MI_slim synonym: "anti tag immunost" EXACT PSI-MI-short [] is_a: MI:0422 ! immunostaining [Term] id: MI:0708 name: monoclonal antibody immunostaining def: "A monospecific antibody for the protein of interest is available, this is used to detect a specific protein within a cell or tissue sample." [PMID:14755292] subset: PSI-MI_slim synonym: "monoclonal immunost" EXACT PSI-MI-short [] is_a: MI:0422 ! immunostaining [Term] id: MI:0709 name: polyclonal antibody immunostaining def: "Immunostaining assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest. These antibodies are used to detect the protein within a cell or tissue sample." [PMID:14755292] subset: PSI-MI_slim synonym: "polyclonal immunost" EXACT PSI-MI-short [] is_a: MI:0422 ! immunostaining [Term] id: MI:0710 name: nucleic acid transformation by treatment with divalent cation def: "Stable introduction and expression of nucleic acid carried out by treatment with divalent cation." [PMID:14755292] subset: PSI-MI_slim synonym: "n transformat cation" EXACT PSI-MI-short [] is_a: MI:0706 ! nucleic acid transformation [Term] id: MI:0711 name: nucleic acid electroporation def: "Electroporation, or electropermeabilization, is a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance inside the cell, such as loading it with a molecular probe, a drug that can change cell's function, or a piece of coding DNA." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl electroporation" EXACT PSI-MI-short [] is_a: MI:0308 ! electroporation is_a: MI:0704 ! nucleic acid delivery [Term] id: MI:0712 name: nucleic acid microinjection def: "Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases nucleic acids." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl microinjection" EXACT PSI-MI-short [] is_a: MI:0311 ! microinjection is_a: MI:0704 ! nucleic acid delivery [Term] id: MI:0713 name: nucleic acid passive uptake def: "Nucleic acid entrance into cells that does not involved specific treatments but rely on natural cellular processes." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl passive uptake" EXACT PSI-MI-short [] is_a: MI:0704 ! nucleic acid delivery is_a: MI:0716 ! passive uptake [Term] id: MI:0714 name: nucleic acid transduction def: "Transduction is the process by which bacterial DNA is moved from one bacterium to another by a virus." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl transduction" EXACT PSI-MI-short [] is_a: MI:0704 ! nucleic acid delivery [Term] id: MI:0715 name: nucleic acid conjugation def: "Bacterial conjugation is the transfer of genetic material between bacteria through cell-to-cell contact. Bacterial conjugation is often incorrectly regarded as the bacterial equivalent of sexual reproduction or mating. It is not actually sexual, as it does not involve the fusing of gametes and the creation of a zygote. It is merely the transfer of a conjugative plasmid from a donor cell to a recipient" [PMID:14755292] subset: PSI-MI_slim synonym: "nucl conjugation" EXACT PSI-MI-short [] is_a: MI:0704 ! nucleic acid delivery [Term] id: MI:0716 name: passive uptake def: "Entrance of molecules into cells that does not involved specific treatments but relies on natural cellular processes." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0307 ! delivery method [Term] id: MI:0717 name: nucleic acid transfection with liposome def: "Lipofection (or liposome transfection) is a technique used to inject genetic material into a cell by means of liposomes which are vesicles that can easily merge with the cell membrane since they are both made of a phospholipid bilayer." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl lipotransfect" EXACT PSI-MI-short [] is_a: MI:0312 ! nucleic acid transfection [Term] id: MI:0718 name: nucleic acid transfection by treatment def: "Transient introduction and expression of nucleic acid carried out by treatment with chemicals." [PMID:14755292] subset: PSI-MI_slim synonym: "n transfection treat" EXACT PSI-MI-short [] is_a: MI:0312 ! nucleic acid transfection [Term] id: MI:0719 name: calcium phosphate nucleic acid transfection def: "Transient introduction and expression of nucleic acid carried out by treatment with calcium phosphate." [PMID:14755292] subset: PSI-MI_slim synonym: "ca po nuc transfect" EXACT PSI-MI-short [] is_a: MI:0718 ! nucleic acid transfection by treatment [Term] id: MI:0720 name: nucleic acid delivery by infection def: "Nucleic acid introduced into a cell via an external organism, usually a virus or bacteria.." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl infection" EXACT PSI-MI-short [] is_a: MI:0310 ! infection is_a: MI:0704 ! nucleic acid delivery [Term] id: MI:0721 name: protein delivery def: "Method by which proteins are delivered into a cell." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0307 ! delivery method [Term] id: MI:0722 name: protein electroporation def: "Method for temporarily permeabilising cell membranes in order to facilitate the entry of a protein." [PMID:14755292] subset: PSI-MI_slim synonym: "prot electroporation" EXACT PSI-MI-short [] is_a: MI:0308 ! electroporation is_a: MI:0721 ! protein delivery [Term] id: MI:0723 name: protein microinjection def: "Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases proteins." [PMID:14755292] subset: PSI-MI_slim synonym: "prot microinjection" EXACT PSI-MI-short [] is_a: MI:0311 ! microinjection is_a: MI:0721 ! protein delivery [Term] id: MI:0724 name: protein delivery by cationic lipid treatment def: "Proteins are delivered into cells by treatment with cationic lipids." [PMID:14755292] subset: PSI-MI_slim synonym: "prot cationic lipid" EXACT PSI-MI-short [] is_a: MI:0721 ! protein delivery [Term] id: MI:0725 name: protein delivery by infection def: "Protein introduced into a cell via an external organism, usually a virus or bacteria." [PMID:14755292] subset: PSI-MI_slim synonym: "prot infection" EXACT PSI-MI-short [] is_a: MI:0310 ! infection is_a: MI:0721 ! protein delivery [Term] id: MI:0726 name: reverse two hybrid def: "Yeast strains are generated in which expression of DB-X/AD-Y or DBPX hybrid proteins is toxic under particular conditions (negative selection). Under these conditions, dissociation of an interaction should provide a selective advantage thereby facilitating detection: a few growing yeast colonies in which DB-X/AD-Y (or DBPX/binding site) fail to interact should be identified among many nongrowing colonies containing interacting DB-X/AD-Y or DBPX/binding site." [PMID:8816797] subset: PSI-MI_slim is_a: MI:0003 ! feature detection method is_a: MI:0232 ! transcriptional complementation assay [Term] id: MI:0727 name: lexa b52 complementation def: "Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), E. coli B42 acidic sequence as the activation domain (AD), and two reporters, lacZ and LEU2, each containing upstream LexA binding elements." [PMID:14613974] subset: PSI-MI_slim synonym: "lexa b52 complement" EXACT PSI-MI-short [] synonym: "LexA B52 transcription complementation" EXACT PSI-MI-alternate [] is_a: MI:0018 ! two hybrid [Term] id: MI:0728 name: gal4 vp16 complementation def: "A chimeric protein consisting of the GAL4 DNA-binding domain (aa 1-147 of GAL4) and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) can specifically activate transcription of a reporter gene located downstream ofGAL4 DNA binding sites and the E1B minimal promoter. Similarly, two chimeric proteins, one encoding a chimeric GAL4 protein and the other encoding a chimeric VP16 protein, can activate the reporter gene, if the domains fused to the GAL4 and VP16 sequences can complex with appropriate conformation. However, if the domains fused to the GAL4 and VP16 sequences do not interact specifically to form a + complex that reconstitutes GAL4 function, the reporter gene cannot be activated." [PMID:1387709] subset: PSI-MI_slim synonym: "gal4 vp16 complement" EXACT PSI-MI-short [] synonym: "karyoplasmic interaction ion strategy" EXACT PSI-MI-alternate [] synonym: "KISS" EXACT PSI-MI-alternate [] synonym: "mammalian two hybrid" EXACT PSI-MI-alternate [] is_a: MI:0018 ! two hybrid [Term] id: MI:0729 name: luminescence based mammalian interactome mapping def: "This strategy uses a luciferase enzyme fused to proteins of interest, which are then coexpressed with individual epitope-tagged partners in mammalian cells. Their interactions are determined by performing an enzymatic assay on anti-tag immunoprecipitates." [PMID:15761153] subset: PSI-MI_slim synonym: "lumier" EXACT PSI-MI-short [] is_a: MI:0004 ! affinity chromatography technology [Term] id: MI:0730 name: pubchem def: "PubChem provides information on the biological activities of small molecules.\nhttp://pubchem.ncbi.nlm.nih.gov/" [PMID:16381840] subset: PSI-MI_slim synonym: "PubChem" EXACT PSI-MI-alternate [] is_a: MI:2054 ! bioactive entity reference [Term] id: MI:0731 name: 3d repertoire def: "The aim of 3D Repertoire is to determine the structures of all amenable complexes in a cell at medium or high resolution, which will later serve to integrate in toponomic and dynamic analyses of protein complexes in a cell. Complex models, EM pictures, expression and purification protocols obtained in the project will be collected in a database connected to the PDB repository." [PMID:14755292] subset: PSI-MI_slim synonym: "3D Repertoire" EXACT PSI-MI-alternate [] is_a: MI:0489 ! source database [Term] id: MI:0732 name: red fluorescent protein tag def: "The red fluorescent protein derived from, for example, marine anemone Discosoma striata and reef corals belonging to the class Anthozoacan can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." [PMID:14755292] subset: PSI-MI_slim synonym: "red fluorescent protein" EXACT PSI-MI-alternate [] synonym: "RFP" EXACT PSI-MI-alternate [] synonym: "rfp tag" EXACT PSI-MI-short [] is_a: MI:0687 ! fluorescent protein tag [Term] id: MI:0733 name: cyan fluorescent protein tag def: "The cyan fluorescent protein derived from Anthozoa reef coral can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." [PMID:14755292] subset: PSI-MI_slim synonym: "CFP" EXACT PSI-MI-alternate [] synonym: "cfp tag" EXACT PSI-MI-short [] synonym: "cyan fluorescent protein" EXACT PSI-MI-alternate [] is_a: MI:0687 ! fluorescent protein tag [Term] id: MI:0734 name: enhanced green fluorescent protein tag def: "Variation of the green fluorescent protein derived from the bioluminescent jellyfish Aequorea victoria, can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." [PMID:14755292] subset: PSI-MI_slim synonym: "EGFP" EXACT PSI-MI-alternate [] synonym: "egfp tag" EXACT PSI-MI-short [] synonym: "enhanced green fluorescent protein" EXACT PSI-MI-alternate [] is_a: MI:0367 ! green fluorescent protein tag [Term] id: MI:0735 name: transactivating tag def: "Tag derived from the transactivating (Tat) protein of human immunodeficiency virus 1 (HIV-1) that can enter cells efficiently when added exogenously in tissue culture. The Tat tag can carry other molecules into cells, by fusion of Tat peptides (residues 1-72 or 37-72,) to any molecule under study. Tat-mediated uptake may allow the delivery of macromolecules previously thought to be impermeable to living cells." [PMID:8290579] subset: PSI-MI_slim synonym: "Tat tag" EXACT PSI-MI-alternate [] synonym: "tat tag" EXACT PSI-MI-short [] is_a: MI:0740 ! cell penetrating peptide tag [Term] id: MI:0736 name: protein passive uptake def: "Proteins entrance into cells that does not involved specific treatments but rely on natural cellular processes." [PMID:14755292] subset: PSI-MI_slim synonym: "prot passive uptake" EXACT PSI-MI-short [] is_a: MI:0716 ! passive uptake is_a: MI:0721 ! protein delivery [Term] id: MI:0737 name: peptide sequence database def: "database storing sequences detected by peptide identification methods." [PMID:14755292] subset: PSI-MI_slim synonym: "pep seq db" EXACT PSI-MI-short [] is_a: MI:0683 ! sequence database [Term] id: MI:0738 name: pride def: "PRIDE is a public repository of protein and peptide identifications for the proteomics community.\nhttp://www.ebi.ac.uk/pride/" [PMID:16381953] subset: PSI-MI_slim xref: search-url: "http://www.ebi.ac.uk/pride/archive/projects/${ac}" is_a: MI:0737 ! peptide sequence database [Term] id: MI:0739 name: penetrating tag def: "Membrane shuttling peptide derived from the Drosophila homeobox protein Antennapedia: RQIKIWFQNRRMKWKK" [PMID:16574060] subset: PSI-MI_slim is_a: MI:0740 ! cell penetrating peptide tag [Term] id: MI:0740 name: cell penetrating peptide tag def: "The peptides named CPPs vary greatly in size, amino acid sequence, and charge, but share the common feature that they have the ability to rapidly translocate the plasma membrane and enable delivery to the cytoplasm or nucleus." [PMID:16574060] subset: PSI-MI_slim synonym: "cell penetrating pep" EXACT PSI-MI-short [] synonym: "cell-penetrating peptides" EXACT PSI-MI-alternate [] synonym: "CPPs" EXACT PSI-MI-alternate [] synonym: "membrane translocating sequences" EXACT PSI-MI-alternate [] synonym: "MTS" EXACT PSI-MI-alternate [] synonym: "protein transduction domains" EXACT PSI-MI-alternate [] synonym: "PTDs" EXACT PSI-MI-alternate [] synonym: "Trojan peptides" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0741 name: peptide atlas def: "PeptideAtlas addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms.\nhttp://www.peptideatlas.org/" [PMID:15642101, PMID:16381952] subset: PSI-MI_slim synonym: "PeptideAtlas" EXACT PSI-MI-alternate [] is_a: MI:0737 ! peptide sequence database [Term] id: MI:0742 name: gpm def: "Global Proteome Machine aim to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results.\nhttp://www.thegpm.org" [PMID:15595733] subset: PSI-MI_slim synonym: "Global Proteome Machine" EXACT PSI-MI-alternate [] is_a: MI:0737 ! peptide sequence database [Term] id: MI:0787 name: genetic experimental form def: "Descriptor of an experimental form involved in a genetic interaction" [PMID:14755292] subset: PSI-MI_slim synonym: "genetic exp form" EXACT PSI-MI-short [] is_a: MI:0346 ! experimental preparation [Term] id: MI:0788 name: knock out def: "The gene has been completely removed e.g. by genetic engineering " [PMID:14755292] subset: PSI-MI_slim synonym: "knock-out" EXACT PSI-MI-short [] is_a: MI:0804 ! mutated gene [Term] id: MI:0789 name: knock down def: "The gene expression has been significantly reduced compared to wild-type by introduction of an external substance, e.g. by RNA interference." [PMID:14755292] subset: PSI-MI_slim synonym: "knock-down" EXACT PSI-MI-short [] is_a: MI:0804 ! mutated gene [Term] id: MI:0790 name: hypermorph def: "The gene function has been partially improved compared to wild-type by altering its sequence." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0787 ! genetic experimental form [Term] id: MI:0791 name: hypomorph def: "The gene function has been partially reduced compared to wild-type by altering its sequence e.g. a temperature sensitive mutant." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0787 ! genetic experimental form [Term] id: MI:0792 name: antimorph def: "The gene function has been antagonized by a mutation in another copy of the gene." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0787 ! genetic experimental form [Term] id: MI:0793 name: amorph def: "The gene function has been abolished by mutation, though the type of mutation is not known." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0787 ! genetic experimental form [Term] id: MI:0794 name: synthetic def: "An effect in which two genetic perturbations, when combined, result in a mutant phenotype that is not observed (to any degree) as a result of any of the individual perturbations.\nwt = a = b = E (not=) ab" [PMID:15833125] subset: PSI-MI_slim synonym: "synthetic genetic interaction (sensu inequality)" EXACT [] synonym: "synthetic genetic interaction defined by inequality" EXACT [] is_a: MI:0933 ! negative genetic interaction [Term] id: MI:0795 name: asynthetic def: "An effect in which individual perturbations of different genes and their combination result in the same mutant phenotype, to the same degree of severity/penetrance. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: \na = b = ab != wt\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim synonym: "asynthetic" EXACT PSI-MI-short [] synonym: "asynthetic genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] is_a: MI:0935 ! positive genetic interaction [Term] id: MI:0796 name: suppression def: "An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than the most severe phenotype of the original perturbations, in effect making the organism more \"wild type\" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\na* < ab <= wt [E = a*]\nOR\nwt <= ab < a* [E = a*]\nwhere 'a*' is the most severe observed phenotype value of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim synonym: "Alleviating interaction" RELATED [] synonym: "suppression" EXACT PSI-MI-short [] synonym: "suppressive genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] is_a: MI:0935 ! positive genetic interaction [Term] id: MI:0797 name: epistasis def: "An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\n(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes." [PMID:15833125] subset: PSI-MI_slim synonym: "epistatic" EXACT PSI-MI-short [] synonym: "epistatic genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] is_a: MI:0208 ! genetic interaction [Term] id: MI:0798 name: conditional genetic interaction defined by inequality def: "The phenotype resulting from genetic perturbation of A has an effect only in the b background, or the b mutant has an effect only in the a background. a has an effect only in the b background, or the b mutant has an effect only in the a background. E. g., WT = a > ab > b or WT > a > b > ab." [PMID:15833125] subset: PSI-MI_slim synonym: "conditional" EXACT PSI-MI-short [] synonym: "conditional genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0799 name: additive genetic interaction defined by inequality def: "Single-mutant phenotype effects combine to give a double-mutant effect different from the wild type and different from single mutant effect. For instance, WT < a = b < ab, b < WT = ab < a, WT < a < b < ab, b < WT < ab < a, and all additional inequalities obtained by interchanging a and b, or reversing the effect of both a and b." [PMID:15833125] subset: PSI-MI_slim synonym: "additive" EXACT PSI-MI-short [] synonym: "additive genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0800 name: single nonmonotonic genetic interaction defined by inequality def: "The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and a backgrounds (for example, b > WT and ab < a); or, a shows opposing effects in the WT and b backgrounds, but not both. E.g., WT > a > ab > b." [PMID:15833125] subset: PSI-MI_slim synonym: "single nonmonotonic" EXACT PSI-MI-short [] synonym: "single nonmonotonic genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0801 name: double nonmonotonic genetic interaction defined by inequality def: "The phenotype resulting from genetic perturbation of both A and B show opposing effects in the WT background and the background with the other mutant gene. E.g., WT >= ab > a >= b" [PMID:15833125] subset: PSI-MI_slim synonym: "double nonmonotonic" EXACT PSI-MI-short [] synonym: "double nonmonotonic genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0802 name: enhancement interaction def: "The A genetic perturbation enhances the phenotype of the B perturbation, or vice versa (e.g. WT = A < B < AB or WT = B < A < AB). This could be conditional or additive by the above scheme.\nOBSOLETE: remap to MI:0933 'negative genetic interaction'" [PMID:15833125] subset: PSI-MI_slim synonym: "enhancement" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0803 name: expression level alteration def: "Synthesis rate of a molecule under investigation differs from its naturally occurring expression level in a cell." [PMID:14755292] subset: PSI-MI_slim synonym: "expression modif" EXACT PSI-MI-short [] is_a: MI:0787 ! genetic experimental form [Term] id: MI:0804 name: mutated gene def: "The gene is mutated in some unknown manner" [PMID:14755292] subset: PSI-MI_slim is_a: MI:0787 ! genetic experimental form [Term] id: MI:0805 name: wwpdb def: "The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community.\nhttp://www.wwpdb.org/" [PMID:14634627] subset: Drugable subset: PSI-MI_slim synonym: "wwPDB" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[0-9][a-zA-Z0-9]{3}" xref: search-url: "http://www.pdbe.org/${ac}" is_a: MI:0447 ! feature database is_a: MI:0461 ! interaction database is_a: MI:0489 ! source database [Term] id: MI:0806 name: pdbj def: "PDBj(Protein Data Bank Japan) maintains the database for the protein structures with financial assistance from the Institute for Bioinformatics Research and Development of Japan Science and Technology Corporation(BIRD-JST), collaborating with the Research Collaboration for Structural Bioinformatics(RCSB) and the MSD in the European Bioinformatics Institute(MSD-EBI) in EU. All three organizations serve as deposition, data processing and distribution sites.\nhttp://www.pdbj.org/" [PMID:12099029] subset: PSI-MI_slim synonym: "PDBj" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[0-9][a-zA-Z0-9]{3}" xref: search-url: "http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/DetailServlet?PDBID=${ac}&PAGEID=Summary" is_a: MI:0805 ! wwpdb [Term] id: MI:0807 name: comigration in gel electrophoresis def: "The interaction of two molecules is determine by their very close proximity or the overlap of their relative bands in a gel." [PMID:14755292] subset: PSI-MI_slim synonym: "comigration in gel" EXACT PSI-MI-short [] is_a: MI:0982 ! electrophoretic mobility-based method [Term] id: MI:0808 name: comigration in sds page def: "Method allowing the detection of strong interactions between two molecules by their very close proximity or the overlap of their relative bands in a denaturing SDS gel." [PMID:14755292, PMID:16732283] subset: PSI-MI_slim synonym: "comigration in sds" EXACT PSI-MI-short [] is_a: MI:0807 ! comigration in gel electrophoresis [Term] id: MI:0809 name: bimolecular fluorescence complementation alt_id: MI:0229 def: "The bimolecular fluorescence complementation (BiFC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two non- fluorescent fragments of a protein fluorophore such as green fluorescent protein (GFP) or its derivatives. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional flourophore that can be identified through fluorescence spectroscopy or microscopy." [PMID:11983170] subset: PSI-MI_slim synonym: "bifc" EXACT PSI-MI-short [] synonym: "gfp complementation" EXACT [] synonym: "green fluorescence protein complementation assay" EXACT [] is_a: MI:0051 ! fluorescence technology is_a: MI:0090 ! protein complementation assay [Term] id: MI:0810 name: substitution analysis def: "In this approach, once a molecule is demonstrated to participate in an interaction, several substitution mutants are produced and tested in the binding assay to identify the residues which identity is crucial for the interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "substitut analysis" EXACT PSI-MI-short [] is_a: MI:0074 ! mutation analysis [Term] id: MI:0811 name: insertion analysis def: "In this approach, once a molecule is demonstrated to participate in an interaction, several insertion derivatives are produced and tested in the binding assay to detect the regions that are important for the interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0074 ! mutation analysis [Term] id: MI:0812 name: calmodulin binding protein tag def: "The protein is expressed and purified as a fusion to the calmoduling-binding protein. The fusion protein can be purified by affinity chromatography using a calmodulin resin." [PMID:14755292] subset: PSI-MI_slim synonym: "cam tag" EXACT PSI-MI-short [] is_a: MI:0240 ! fusion protein [Term] id: MI:0813 name: proximity ligation assay def: "Upon binding of two proximity probes (usually antibodies conjugated to DNA) to the same target protein complex, the oligonucleotides on the proximity probes are brought close together. These antibody-conjugated oligonucleotides hybridize to two connector oligonucleotides that are ligated to form a circular DNA molecule. This newly formed DNA-molecule can be amplified by rolling circle amplification. The resulting single-stranded DNA-molecule collapses into a bundle, which is detectable through hybridization of fluorescently labeled complementary oligonucleotides." [PMID:15155907, PMID:\:17072308] subset: PSI-MI_slim synonym: "in situ proximity ligation assay" RELATED [] synonym: "p elisa" EXACT [] synonym: "pELISA" EXACT PSI-MI-alternate [] synonym: "PLA" EXACT PSI-MI-short [] synonym: "pLISA" RELATED [] synonym: "proximity ligation" RELATED [] is_a: MI:0400 ! affinity technology is_a: MI:0421 ! identification by antibody [Term] id: MI:0814 name: protease accessibility laddering def: "In protease accessibility laddering (PAL) tagged proteins are purified on magnetic beads in their natively folded state. While attached to the beads, proteins are probed with proteases. Proteolytic fragments are eluted and detected by immunoblotting with antibodies against the tag (e.g., Protein A, GFP, and 6xHis)." [PMID:16615907] subset: PSI-MI_slim synonym: "pal" EXACT PSI-MI-alternate [] synonym: "protease access" EXACT PSI-MI-short [] is_a: MI:0605 ! enzymatic footprinting [Term] id: MI:0815 name: confirmation by molecular weight def: "Molecule whose sequence identity is derived from their molecular weight" [PMID:14755292] subset: PSI-MI_slim synonym: "weight identificat" EXACT PSI-MI-short [] is_a: MI:0396 ! predetermined participant [Term] id: MI:0816 name: molecular weight estimation by staining def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker." [PMID:14755292] subset: PSI-MI_slim synonym: "weight by staining" EXACT PSI-MI-short [] is_a: MI:0815 ! confirmation by molecular weight [Term] id: MI:0817 name: molecular weight estimation by silver staining def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with silver." [PMID:14755292] subset: PSI-MI_slim synonym: "weight silver stain" EXACT PSI-MI-short [] is_a: MI:0816 ! molecular weight estimation by staining [Term] id: MI:0818 name: molecular weight estimation by coomasie staining def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with comassie dye." [PMID:14755292] subset: PSI-MI_slim synonym: "weight by comassie" EXACT PSI-MI-short [] is_a: MI:0816 ! molecular weight estimation by staining [Term] id: MI:0819 name: molecular weight estimation by bromide staining def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with bromide dyes." [PMID:14755292] subset: PSI-MI_slim synonym: "weight by bromide" EXACT PSI-MI-short [] is_a: MI:0816 ! molecular weight estimation by staining [Term] id: MI:0820 name: molecular weight estimation by sybr staining def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with sybr dyes." [PMID:14755292] subset: PSI-MI_slim synonym: "safe DNA gel stain" EXACT PSI-MI-alternate [] synonym: "weight by sybr" EXACT PSI-MI-short [] is_a: MI:0816 ! molecular weight estimation by staining [Term] id: MI:0821 name: molecular weight estimation by autoradiography def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining by autoradiography." [PMID:14755292] subset: PSI-MI_slim synonym: "weight autoradiogra" EXACT PSI-MI-short [] is_a: MI:0815 ! confirmation by molecular weight [Term] id: MI:0822 name: molecular weight estimation by hoechst staining def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with Hoechst dyes." [PMID:14755292] subset: PSI-MI_slim synonym: "weight by hoechst" EXACT PSI-MI-short [] is_a: MI:0816 ! molecular weight estimation by staining [Term] id: MI:0823 name: predetermined feature def: "Feature detection not verified in the context of an experiment but assumed from external or previous experimental evidence(s)." [PMID:14755292] subset: PSI-MI_slim synonym: "predetermined featur" EXACT PSI-MI-short [] is_a: MI:0093 ! protein sequence identification is_a: MI:0427 ! Identification by mass spectrometry is_a: MI:0659 ! experimental feature detection [Term] id: MI:0824 name: x-ray powder diffraction def: "Analysis of a diffraction pattern generated by an isotropic sample composed of many randomly oriented crystals." [PMID:14755292] subset: PSI-MI_slim synonym: "X-ray" EXACT PSI-MI-alternate [] synonym: "x-ray powder diffrac" EXACT PSI-MI-short [] is_a: MI:0114 ! x-ray crystallography [Term] id: MI:0825 name: x-ray fiber diffraction def: "Analysis of the diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using X-ray." [PMID:14755292] subset: PSI-MI_slim synonym: "X-ray" EXACT PSI-MI-alternate [] synonym: "x-ray fiber diffrac" EXACT PSI-MI-short [] is_a: MI:0114 ! x-ray crystallography [Term] id: MI:0826 name: x ray scattering def: "Method where the internal structure of a sample is derived from the intensity distribution of the scattered monochromatic X-ray beam at very low scattering angles." [PMID:14755292] subset: PSI-MI_slim synonym: "saxs" EXACT PSI-MI-short [] is_a: MI:0067 ! light scattering [Term] id: MI:0827 name: x-ray tomography def: "X-ray Tomography is a branch of X-ray microscopy. A series of projection images are used to calculate a three dimensional reconstruction of an object. The technique has found many applications in materials science and later in biology and biomedical research. In terms of the latter, the National Center for X-ray Tomography (NCXT) is one of the principle developers of this technology, in particular for imaging whole, hydrated cells." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0428 ! imaging technique [Term] id: MI:0828 name: polyprotein fragment def: "Subpart of a polyprotein that is naturally cleaved in vivo." [PMID:14577292] subset: PSI-MI_slim synonym: "chain" RELATED [] synonym: "polyprotein frag" EXACT PSI-MI-short [] is_a: MI:0252 ! biological feature [Term] id: MI:0829 name: multiple parent reference def: "This qualifier is used for hybrid or composite molecules with more than one cross-reference to parent molecules." [PMID:14755292] subset: PSI-MI_slim synonym: "multiple parent" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0830 name: tissue list def: "List of tissue used as topic in UniProt RC line.\nhttp://www.expasy.org/cgi-bin/lists?tisslist.txt" [PMID:14755292] subset: PSI-MI_slim is_a: MI:0473 ! participant database [Term] id: MI:0831 name: cell ontology def: "Ontology of cell types.\nhttp://obo.sourceforge.net/cgi-bin/detail.cgi?cell" [PMID:16381901] subset: PSI-MI_slim is_a: MI:0473 ! participant database [Term] id: MI:0832 name: half cystine def: "A protein modification that is effectively either one half of a cystine cross-link, or a cysteine residue with one hydrogen atom or proton removed" [MOD:00798, RESID:AA0025] synonym: "Half of a disulfide bridge" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0833 name: autoradiography def: "Experimental method by which radiolabel is detected by exposure to a photographic emulsion forming a pattern on the film." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0659 ! experimental feature detection is_a: MI:0866 ! tag visualisation [Term] id: MI:0834 name: ka def: "Association rate constant or rate of complex formation. Unit MOLE per SECOND (M-1 s-1)" [PMID:14755292] subset: PSI-MI_slim synonym: "kon" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:0835 name: koff def: "Dissociation rate constant measuring the stability of a complex. Unit SECOND (s-1)" [PMID:14755292] subset: PSI-MI_slim synonym: "Kd" RELATED [] synonym: "koff" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:0836 name: temperature of interaction def: "Temperature at which interaction was determined. Unit KELVIN (K)" [PMID:14755292] subset: PSI-MI_slim synonym: "T interaction" EXACT PSI-MI-alternate [] synonym: "temp interaction" EXACT PSI-MI-short [] synonym: "Tint" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:0837 name: pH of interaction def: "pH at which interaction was determined." [PMID:14755292] subset: PSI-MI_slim synonym: "pHint" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:0838 name: kelvin def: "A scale that measures an object's temperature over absolute zero, the theoretical coolest temperature where all molecular and atomic motion ceases. On the Kelvin scale, the freezing point of water is 273 (273 K = 0 o C = 32 o F)." [PMID:14755292] subset: PSI-MI_slim synonym: "K" EXACT PSI-MI-alternate [] is_a: MI:0647 ! parameter unit [Term] id: MI:0839 name: per mole per second def: "Per mole per second, unit for association rate constant." [PMID:14755292] subset: PSI-MI_slim synonym: "M-1s-1" EXACT PSI-MI-alternate [] is_a: MI:0647 ! parameter unit [Term] id: MI:0840 name: stimulator def: "Molecule stimulating an interaction by interacting with one or more of the participants." [PMID:14755292] subset: PSI-MI_slim is_a: MI:2274 ! regulator [Term] id: MI:0841 name: phosphotransferase assay def: "Measures the rate of a phosphate transfer between two molecules." [PMID:14755292] subset: PSI-MI_slim synonym: "phosphotransfer assay" RELATED [] synonym: "phosphotransferase" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study [Term] id: MI:0842 name: phosphate donor def: "Any molecule that is able to transfer a phosphate group to another chemical species." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0918 ! donor [Term] id: MI:0843 name: phosphate acceptor def: "Molecule to which a phosphate group may be transferred from a phosphate donor." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0919 ! acceptor [Term] id: MI:0844 name: phosphotransfer reaction def: "Reaction where a phosphate is transferred between two proteins of a phosphorelay system." [PMID:14755292, PMID:16712436] subset: PSI-MI_slim synonym: "phosphotransfer" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0845 name: spin label def: "Paramagnetic fragment, most often a cyclic nitroxide derivative, covalently attached to a molecule of interest." [PMID:10966640] subset: PSI-MI_slim is_a: MI:0505 ! experimental feature [Term] id: MI:0846 name: r1 spin label def: "Paramagnetic molecule (1-oxyl-2,2,5,5-tetramethylpyrroline-\n3-methyl)-methanethiosulfonate. that can be covalently attached to any cysteine aminoacid producing a nitroxide\nside chain designated R1." [PMID:10966640] subset: PSI-MI_slim is_a: MI:0845 ! spin label [Term] id: MI:0847 name: dansyl label def: "Dansyl is the acronym of 5-dimethylaminonaphthalene-1-sulfonyl radical group reacting with any NH2 groups." [PMID:14755292] subset: PSI-MI_slim synonym: "5-dimethylaminonaphthalene-1-sulfonyl tag" EXACT PSI-MI-alternate [] synonym: "dansyl tag" EXACT PSI-MI-alternate [] is_a: MI:0857 ! fluorescent dye label [Term] id: MI:0848 name: 125i radiolabel def: "Molecule labelled with 125 radio isotope of iodine atoms." [PMID:14755292] subset: PSI-MI_slim synonym: "125I" EXACT PSI-MI-alternate [] synonym: "I125" EXACT PSI-MI-alternate [] is_a: MI:0517 ! radiolabel [Term] id: MI:0849 name: ncbi taxonomy def: "The NCBI taxonomy database indexes over 55 000 organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The Taxonomy Browser can be used to view the taxonomic position or retrieve sequence and structural data for a particular organism or group of organisms. Searches of the NCBI taxonomy may be made on the basis of whole or partial organism names, and direct links to organisms commonly used in biological research are also provided. The Taxonomy Browser can also be used to display the number of nucleic acid sequences, protein sequences, and protein structures available for organisms included in the branch. From the data display for a particular organism, one can retrieve and download the sequence data for that organism, or protein 3D structure data if available.\nhttp://www.ncbi.nlm.nih.gov/Taxonomy/" [PMID:10592169] subset: PSI-MI_slim xref: id-validation-regexp: "[0-9]+" xref: search-url: "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=${ac}&lvl=3&lin=f&keep=1&srchmode=1&unlock" is_a: MI:0473 ! participant database [Term] id: MI:0850 name: encode def: "ENCODE (the Encyclopedia Of DNA Elements) seeks to identify all protein-coding genes. The current ENCODE data set is derived from 1% of the human genome and has been selected for analysis in the pilot phase of the project.\nhttp://www.genome.gov/10005107" [PMID:17372197] subset: PSI-MI_slim synonym: "ENCODE" EXACT PSI-MI-alternate [] synonym: "Encyclopedia Of DNA Elements" EXACT PSI-MI-alternate [] is_a: MI:1094 ! genome databases [Term] id: MI:0851 name: protein genbank identifier def: "GenBank Identifier or GI numbers for proteins." [PMID:17170002] subset: PSI-MI_slim synonym: "GenBank Protein GI" EXACT PSI-MI-alternate [] synonym: "genbank protein gi" EXACT PSI-MI-alternate [] synonym: "genbank_protein_gi" EXACT PSI-MI-short [] synonym: "genpept id" EXACT [] xref: id-validation-regexp: "[0-9]+" xref: search-url: "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=Retrieve&dopt=Graphics&list_uids=${ac}" is_a: MI:0860 ! genbank identifier [Term] id: MI:0852 name: nucleotide genbank identifier def: "GenBank Identifier or GI numbers for nucleotide." [PMID:17170002] subset: PSI-MI_slim synonym: "genbank nucleotide" EXACT PSI-MI-alternate [] synonym: "GenBank Nucleotide" EXACT PSI-MI-alternate [] synonym: "genbank_nucl_gi" EXACT PSI-MI-short [] xref: id-validation-regexp: "[0-9]+" xref: search-url: "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=Retrieve&dopt=Graphics&list_uids=$" is_a: MI:0860 ! genbank identifier [Term] id: MI:0853 name: dna overhang def: "An overhang is a stretch of unpaired nucleotides in the end of a DNA molecule. These unpaired nucleotides can be in either strand, creating either 3' or 5' overhangs. Longer overhangs are called cohessive ends or sticky ends. They are most often created by restriction endonucleases when they cut DNA. Very often they cut the two DNA strands four base pairs from each other, creating a four-base 3' overhang in the other molecule and a complementary 5' overhang in the other. These ends are called cohessive since they are easily joined back together by a ligase" [PMID:14755292] subset: PSI-MI_slim synonym: "cohessive ends" EXACT PSI-MI-alternate [] synonym: "sticky ends" EXACT PSI-MI-alternate [] is_a: MI:0505 ! experimental feature [Term] id: MI:0854 name: 3 prime overhang def: "An overhang is a stretch of unpaired nucleotides in the end of a 3' strand of a DNA molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "3 prime sticky end" EXACT PSI-MI-alternate [] is_a: MI:0853 ! dna overhang [Term] id: MI:0855 name: 5 prime overhang def: "An overhang is a stretch of unpaired nucleotides in the end of a 5' strand of a DNA molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "5 prime sticky end" EXACT PSI-MI-alternate [] is_a: MI:0853 ! dna overhang [Term] id: MI:0856 name: fluorophore def: "A fluorophore is a component of a molecule which causes a molecule to be fluorescent. It is a functional group in a molecule which will absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. The amount and wavelength of the emitted energy depend on both the fluorophore and the chemical environment of the fluorophore." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0505 ! experimental feature [Term] id: MI:0857 name: fluorescent dye label def: "Dye label containing a fluorophore which absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength." [PMID:14755292] subset: PSI-MI_slim synonym: "fluorescent dye" EXACT PSI-MI-short [] is_a: MI:0373 ! dye label is_a: MI:0856 ! fluorophore [Term] id: MI:0858 name: immunodepleted coimmunoprecipitation def: "Method involving consecutive coimmunoimmunoprecipitations on the same sample, a control where an interaction is detected, and other CoIPs where the sample is previously treated with a specific antibody that precipitates a candidate interactor and leads to the suppression of an interaction or a change in composition of a complex." [PMID:17081976] subset: PSI-MI_slim synonym: "immunodepleted coip" EXACT PSI-MI-alternate [] synonym: "immunodepletion" EXACT PSI-MI-short [] is_a: MI:0019 ! coimmunoprecipitation [Term] id: MI:0859 name: force spectroscopy def: "A single-molecule technique that measures the behavior of a molecular complex under stretching or torsional mechanical force." [PMID:18511917] synonym: "force measurement" RELATED [] synonym: "intermolecular force" EXACT PSI-MI-alternate [] synonym: "molecular force measurement" RELATED [] synonym: "single molecule force measurement" RELATED [] synonym: "surface adhesion force measurement" RELATED [] is_a: MI:0013 ! biophysical is_a: MI:2318 ! force measurement [Term] id: MI:0860 name: genbank identifier def: " edit" [PMID:15078858] subset: PSI-MI_slim xref: id-validation-regexp: "ENS[A-Z]+[0-9]{11}" is_a: MI:0683 ! sequence database [Term] id: MI:0861 name: protein a tag def: "The protein A is a bacterial cell wall isolated from Staphylococcus aureus that binds to mammalian IgGs mainly through Fc regions. The protein A can be use to retaint antibodies or as fusion tag of a protein under analysis." [PMID:14755292] subset: PSI-MI_slim synonym: "protein A" EXACT PSI-MI-alternate [] is_a: MI:0240 ! fusion protein [Term] id: MI:0862 name: zz tag def: "The ZZ tag is a tag made out of two tandem repeats of the Protein A IgG binding domain. " [PMID:11694505] subset: PSI-MI_slim synonym: "ZZ tag" EXACT PSI-MI-alternate [] is_a: MI:0861 ! protein a tag [Term] id: MI:0863 name: thiol reactive lanthanide label def: "Thiol-reactive lanthanide complexes have been synthesized that are luminescent when bound to terbium and/or europium. The Tb3+-DTPA-cs124-EMCH complexes consist of a diethylenetriaminepentaacetate (DTPA) chelate covalently joined through one amide bond to a chromophore, carbostyril 124, and via a second amide bond to a maleimide, bromoacetamide, or pyridyldithio moiety. This label can be Site-specific attached to both proteins and DNA." [PMID:10077482] subset: PSI-MI_slim synonym: "Tb3+-DTPA-cs124-EMCH" EXACT PSI-MI-alternate [] synonym: "thiol lanthanide" EXACT PSI-MI-short [] is_a: MI:1256 ! luminscent dye label [Term] id: MI:0864 name: brenda def: "A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.\nhttp://www.brenda-enzymes.info" [PMID:14755292] subset: PSI-MI_slim is_a: MI:0473 ! participant database [Term] id: MI:0865 name: fluorescence acceptor donor pair def: "Pair of fluorophores attached to the same molecule used in a fret experiment to observe the details of conformational changes ." [PMID:14755292] subset: PSI-MI_slim synonym: "fret pair" EXACT PSI-MI-short [] is_a: MI:0495 ! experimental role [Term] id: MI:0866 name: tag visualisation def: "Molecule whose sequence identity is not checked after the interaction but its presence is detected through its tag." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0396 ! predetermined participant [Term] id: MI:0867 name: tag visualisation by fluorescence def: "The molecule is produced fused to a tag containing a fluorophore, such as GFP tagged to a recombinant protein, or a fluorophore has been chemically attached to the molecule. Subsequence observation or measurement of fluorescence is used to identify the presence of the molecule in an interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "tag fluorescence" EXACT PSI-MI-short [] is_a: MI:0866 ! tag visualisation [Term] id: MI:0868 name: author identifier def: "Author published identifier." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0869 name: originally assigned identifier def: "Identifier assigned when the record was created by a source database." [PMID:14755292] subset: PSI-MI_slim synonym: "original identifier" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0870 name: demethylase assay def: "Measures the catalysis of the hydrolysis of an methyl group from a substrate molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study [Term] id: MI:0871 name: demethylation reaction def: "The cleavage of a methyl group from a polypeptide. Methylation is generally an irreversible reaction except in mamalian." [GO:0006482, PMID:17277772] subset: PSI-MI_slim synonym: "demethylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0872 name: atomic force microscopy def: "The atomic force microscope (AFM) is a very high-resolution type of scanning probe microscope, with demonstrated resolution of fractions of a nanometer, more than 1000 times better than the optical diffraction limit. The AFM was invented by Binnig, Quate and Gerber in 1986, and is one of the foremost tools for imaging, measuring and manipulating matter at the nanoscale.The term 'microscope' in the name is actually a misnomer because it implies looking, while in fact the information is gathered by feeling out the surface with a mechanical feeler.\nhttp://en.wikipedia.org/wiki/Atomic_force_microscope" [PMID:17502105] subset: PSI-MI_slim synonym: "AFM" EXACT PSI-MI-alternate [] synonym: "atomic force microsc" EXACT PSI-MI-short [] is_a: MI:0428 ! imaging technique [Term] id: MI:0873 name: curation request def: "Annotation of a published paper which has been externally requested." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1093 ! bibliographic attribute name [Term] id: MI:0875 name: dataset def: "Targeted curation dataset grouping experiments by topic or dataset origin." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1093 ! bibliographic attribute name [Term] id: MI:0878 name: author submitted def: "Data directly submitted by the authors to a database prior to publication." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0665 ! experiment attribute name [Term] id: MI:0879 name: nucleoside triphosphatase assay def: "Measures the catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate." [PMID:14755292] subset: PSI-MI_slim synonym: "triphosphatase ass" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study is_a: MI:0434 ! phosphatase assay [Term] id: MI:0880 name: atpase assay def: "Measures the catalysis of the hydrolysis of ATP+ H2O = ADP + phosphate." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0879 ! nucleoside triphosphatase assay [Term] id: MI:0881 name: nucleoside triphosphatase reaction def: "Catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate." [GO:0017111, PMID:14755292] subset: PSI-MI_slim synonym: "triphosphatase react" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0882 name: atpase reaction def: "Catalysis of the hydrolisis of ATP+ H2O = ADP + phosphate." [GO:0016887, PMID:14755292] subset: PSI-MI_slim is_a: MI:0881 ! nucleoside triphosphatase reaction [Term] id: MI:0883 name: gtpase reaction def: "Catalysis of the hydrolisis of GTP+ H2O = GDP + phosphate." [GO:0003924, PMID:14755292] subset: PSI-MI_slim is_a: MI:0881 ! nucleoside triphosphatase reaction [Term] id: MI:0884 name: vsv tag def: "Epitope tag derived from vesicular stomatitis virus (VSV) glycoprotein. The tag sequence is YTDIEMNRLGK and many antibodies against it are commercially available." [PMID:14755292] subset: PSI-MI_slim synonym: "vesicular stomatitis virus tag" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0885 name: journal def: "Name and details of a journal from which paper has been taken." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1093 ! bibliographic attribute name [Term] id: MI:0886 name: publication year def: "Year of publication of a paper." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1093 ! bibliographic attribute name [Term] id: MI:0887 name: histone acetylase assay def: "In histone acetylation the histones are acetylated on lysine residues in the N-terminal tail as part of gene regulation. Typically, these reactions are catalyzed by enzymes with \"histone acetyltransferase\" (HAt)" [PMID:14755292] subset: PSI-MI_slim synonym: "HAt" EXACT PSI-MI-alternate [] synonym: "hat" EXACT PSI-MI-short [] synonym: "histone acetylation" RELATED [] is_a: MI:0889 ! acetylase assay [Term] id: MI:0888 name: small angle neutron scattering def: "During a SANS experiment a beam of neutrons is directed at a sample. The neutrons are elastically scattered by a sample and the resulting scattering pattern is analyzed to provide information about the size, shape and orientation of some component of the sample." [PMID:11578931] subset: PSI-MI_slim synonym: "SANS" EXACT PSI-MI-alternate [] synonym: "sans" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical [Term] id: MI:0889 name: acetylase assay def: "Measures the catalysis of the addition of an acetyl group to a target molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "acetylation" RELATED [] is_a: MI:0415 ! enzymatic study [Term] id: MI:0890 name: qdot def: "Qdot are nanocrystals fluorophores . Nanocrystals a are extremely efficient materials for generating and they have a highly customizable surface for directing their bioactivity, producing a fluorescent probe that outperforms traditional dyes in many fluorescence applications." [PMID:17569782] subset: PSI-MI_slim is_a: MI:0857 ! fluorescent dye label [Term] id: MI:0891 name: neutron fiber diffraction def: "Analysis of diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using neutron beam." [PMID:10771422, PMID:15272083, PMID:15546977, PMID:15914673, PMID:16041074, PMID:16707576] subset: PSI-MI_slim synonym: "neutron fiber diff" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical [Term] id: MI:0892 name: solid phase assay def: "Assay where at least one molecule under analysis is bound to a solid surface, such as a microplate wall or the sides of a tube, the other reactants being free in solution." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0400 ! affinity technology [Term] id: MI:0893 name: neutron diffraction def: "Analysis of diffraction pattern using neutron beam" [PMID:10771422, PMID:15272083, PMID:15546977, PMID:15914673, PMID:16041074, PMID:16707576] subset: PSI-MI_slim is_a: MI:0013 ! biophysical [Term] id: MI:0894 name: electron diffraction def: "Analysis of diffraction pattern using electron beam." [PMID:10949309, PMID:11034202, PMID:11171962, PMID:11532455, PMID:11700061, PMID:15141214, PMID:16325200] subset: PSI-MI_slim is_a: MI:0013 ! biophysical [Term] id: MI:0895 name: protein kinase A complementation def: "This method uses Renilla luciferase (Rluc)-based protein fragment complementation assay (PCA) that is designed specifically to investigate dynamic protein complexes (association and dissociation). It is chose to generate a PCA based on the Rluc, which is, because of its simplicity and sensitivity, a widely used bioluminescence reporter. The general scheme for construction and detection of the Rluc-PCA PKA sensor consists of fusing complementary fragments of Rluc to the regulatory (Reg) and catalytic (Cat) PKA subunits of PKA." [PMID:17942691] subset: PSI-MI_slim synonym: "pka complementation" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0896 name: renilla luciferase protein tag def: "Renilla luciferase, is an enzyme of the sea pansy catalyzing the oxidation of the coelenterazine pigment) that produces light. Renilla luciferase produces a blue light of 480nm." [PMID:14755292] subset: PSI-MI_slim synonym: "renilla luciferase" EXACT PSI-MI-short [] is_a: MI:1205 ! luciferase tag [Term] id: MI:0897 name: protein modification ontology def: "Catalogue of covalent modification of, or a change resulting in an alteration of the measured molecular mass of, a peptide or protein amino acid residue." [PMID:14755292] subset: PSI-MI_slim synonym: "psi-mod" EXACT PSI-MI-short [] xref: id-validation-regexp: "MOD:[0-9]{5}" is_a: MI:0447 ! feature database [Term] id: MI:0898 name: putative self def: "Molecule that is reported to self-interact but the experimental condition does not allow to resolve whether the interaction is intramolecular (true self interaction) or intermolecular (homodimer)." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role is_a: MI:0500 ! biological role [Term] id: MI:0899 name: p3 filamentous phage display def: "pIII is one of the minor coat proteins that decorates in five copies the emerging tip of filamentous phage. Similarly to pVIII pIII also tolerates peptide insertions at the amino-terminus. The sequences to be displayed can either be encoded in the phage copy of the coat gene or in an extra pIII gene copy carried on a phagemid. In the first case 5 copies o the hybrid proteins are displayed while in the latter only a few capsid display one copy and the majority display none. Because of the low copy number pIII display is often referred to as low valency display." [PMID:1696028] subset: PSI-MI_slim synonym: "low valency display" EXACT PSI-MI-alternate [] synonym: "p3 filamentous phage" EXACT PSI-MI-short [] is_a: MI:0048 ! filamentous phage display [Term] id: MI:0900 name: p8 filamentous phage display def: "pVIII is the major coat protein of filamentous phage. Its amino-terminus is exposed to solvent and tolerates the insertion of relatively large peptide fragments. By inserting the peptide coding sequence into the phage copy of the pVIII gene up to 3000 copies of the hybrid proteins can be displayed along the phage capsid. Alternatively the hybrid protein can be encoded on a phagemid that is incorporated in a virus like particle by infection with a helper phage. In this latter case one obtains a chimeric capsid where hybrid proteins are interspersed at different density in an otherwise wild type coat. Because of the high copy number pVIII display is also referred to as high valency display." [PMID:1720463] subset: PSI-MI_slim synonym: "high valency display" EXACT PSI-MI-alternate [] synonym: "p8 filamentous phage" EXACT PSI-MI-short [] is_a: MI:0048 ! filamentous phage display [Term] id: MI:0901 name: isotope label footprinting def: "Exposed amino acid residues undergo a rapid exchange of a specific radio-isotope e.g. hydrogen/deuterium. Residues involved in a molecular interaction are protected from this exchange and exhibit a much slower rate of exchange. This method of binding range identification must be coupled to NMR or mass spectrometry technologies in order to detect the radio-isotope exchange." [PMID:18184591] subset: PSI-MI_slim synonym: "isotope footprinting" EXACT PSI-MI-short [] is_a: MI:0605 ! enzymatic footprinting [Term] id: MI:0902 name: rna cleavage def: "Any process by which an RNA molecule is cleaved at specific sites or in a regulated manner." [GO:0006396, PMID:14681407] subset: PSI-MI_slim is_a: MI:0910 ! nucleic acid cleavage [Term] id: MI:0903 name: mpidb def: "The microbial protein-protein interactions database (MPDIB) aims to collect and provide all known physical prokaryotic interactions. Note as of 2013, this database is no longer active, but all IMEx curation was imported and is now maintained by the IntAct database (www.ebi.ac.uk/intact)." [PMID:14755292] subset: PSI-MI_slim synonym: "MPDIB" EXACT PSI-MI-alternate [] is_a: MI:0461 ! interaction database is_a: MI:0973 ! imex source [Term] id: MI:0904 name: polysaccharide def: "A polysaccharide is a complex polymer of carbohydrate monormers. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1100 ! bioactive entity [Term] id: MI:0905 name: amplified luminescent proximity homogeneous assay def: "AlphaScreen relies on the use of Donor and Acceptor beads that are coated with a layer of hydrogel providing functional groups for bioconjugation. When a biological interaction between molecules brings the beads into proximity, a cascade of chemical reactions is initiated to produce a greatly amplified signal. Upon laser excitation, a photosensitizer in the Donor bead converts ambient oxygen to a more excited singlet state. The singlet state oxygen molecules diffuse across to react with a chemiluminescer in the Acceptor bead that further activates fluorophores contained within the same bead. The fluorophores subsequently emit light at 520-620 nm. In the absence of a specific biological interaction, the singlet state oxygen molecules produced by the Donor bead go undetected without the close proximity of the Acceptor bead. AlphaScreen has successfully been developed for enzyme assays (kinase, helicase, protease, ...), interaction assays (ligand/receptor, protein/protein, protein/DNA), immunoassays, and GPCR functional assays (cAMP, IP3)." [PMID:17092917] subset: PSI-MI_slim synonym: "alfa-screen" EXACT PSI-MI-short [] synonym: "AlphaScreen" EXACT PSI-MI-alternate [] is_a: MI:0051 ! fluorescence technology [Term] id: MI:0906 name: au1 tag def: "The protein of interest is expressed as a fusion to the peptide DTYRYI for which antibodies are commercially available." [PMID:18216269] subset: PSI-MI_slim synonym: "DTYRYI epitope tag" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0907 name: conformational status def: "Statement about the native/denatured conformation of the protein." [PMID:14755292] subset: PSI-MI_slim synonym: "conformation" EXACT PSI-MI-short [] is_a: MI:0346 ! experimental preparation [Term] id: MI:0908 name: denatured def: "Altered conformation state of the protein as a result of heat or chemical modification resulting in a changed structure of the protein." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0907 ! conformational status [Term] id: MI:0909 name: native def: "State of the protein without interference i.e. the natural form." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0907 ! conformational status [Term] id: MI:0910 name: nucleic acid cleavage def: "Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments." [PMID:14755292] subset: PSI-MI_slim synonym: "ncl acid cleavage" EXACT PSI-MI-short [] is_a: MI:0194 ! cleavage reaction [Term] id: MI:0911 name: cross linker def: "A variety of crosslinkers are used to analyze subunit structure of proteins, protein interactions and various parameters of protein function. Subunit structure is deduced since crosslinkers only bind surface amino residues in relatively close proximity in the native state. Protein interactions are often too weak or transient to be easily detected, but by crosslinking, the interactions can be captured and analyzed." [PMID:14755292] subset: PSI-MI_slim synonym: "crosslinker" EXACT PSI-MI-alternate [] is_a: MI:0505 ! experimental feature [Term] id: MI:0912 name: spdp cross linker def: "N -Succinimidyl 3-(2-pyridyldithio)-propionate, is heterobifunctional, thiol-cleavable \nand membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester \nthat will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond." [PMID:17360572] subset: PSI-MI_slim synonym: "N -Succinimidyl 3-(2-pyridyldithio)-propionate" EXACT PSI-MI-alternate [] is_a: MI:0911 ! cross linker [Term] id: MI:0913 name: lc-spdp cross linker def: "Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate, is an heterobifunctional, thiol-cleavable \nand membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester \nthat will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond. LC-SPDP is a derivative of the classical SPDP with a longer spacer arm." [PMID:17360572] subset: PSI-MI_slim synonym: "Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate" EXACT PSI-MI-alternate [] is_a: MI:0912 ! spdp cross linker [Term] id: MI:0914 name: association def: "Interaction between molecules that may participate in formation of one, but possibly more, physical complexes. Often describes a set of molecules that are co-purified in a single pull-down or coimmunoprecipitation but might participate in formation of distinct physical complexes sharing a common bait." [PMID:14755292] subset: PSI-MI_slim is_a: MI:2232 ! molecular association [Term] id: MI:0915 name: physical association def: "Interaction between molecules within the same physical complex. Often identified under conditions which suggest that the molecules are in close proximity but not necessarily in direct contact with each other." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0914 ! association [Term] id: MI:0916 name: lexa vp16 complementation def: "Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) that can specifically activate transcription of a reporter gene located downstream." [PMID:9371806] subset: PSI-MI_slim synonym: "lexa vp16 complement" EXACT PSI-MI-short [] synonym: "LexA VP16 transcription complementation" EXACT PSI-MI-alternate [] is_a: MI:0018 ! two hybrid [Term] id: MI:0917 name: matrixdb def: "Knowledgebase of the extracellular matrix storing experimentally determined interactions involving extracellular biomolecules. It includes protein-protein, protein-polysaccharide, and protein-lipid interactions." [PMID:19147664] subset: PSI-MI_slim xref: search-url: "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=${ac}" is_a: MI:0461 ! interaction database is_a: MI:0973 ! imex source [Term] id: MI:0918 name: donor def: "Molecule which emits electrons or ions that are transfered to an acceptor molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0500 ! biological role [Term] id: MI:0919 name: acceptor def: "Molecule able to receive electrons or ions from a donor molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0500 ! biological role [Term] id: MI:0920 name: ribonuclease assay def: "Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of RNA." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1034 ! nuclease assay [Term] id: MI:0921 name: surface plasmon resonance array def: "This array technology allows the screening of binding abilities of hundreds or thousands of biomolecules (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) printed onto the gold-coated chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with a non-labelled sample (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) to identify the baits that can bind to it. This is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation on each spot." [PMID:16510109, PMID:16837183, PMID:17889820] subset: PSI-MI_slim synonym: "Biacore Flexchip(r)" EXACT PSI-MI-alternate [] synonym: "spr array" EXACT PSI-MI-short [] synonym: "SPRi-Plex " EXACT PSI-MI-alternate [] synonym: "SPRImager" EXACT PSI-MI-alternate [] is_a: MI:0008 ! array technology is_a: MI:0107 ! surface plasmon resonance [Term] id: MI:0922 name: imex evidence def: "Experimental evidence supporting an interaction curated and released under the IMEx agreement." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0923 name: irefindex def: "iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once.\nhttp://irefindex.uio.no/" [PMID:18823568] subset: PSI-MI_slim synonym: "iRefIndex" EXACT PSI-MI-alternate [] is_a: MI:0461 ! interaction database is_a: MI:0489 ! source database [Term] id: MI:0924 name: camjedb def: "Camjedb is a comprehensive database for information on the genome of Campylobacter jejuni.\nhttp://www.sanger.ac.uk/Projects/C_jejuni/" [PMID:106882042] subset: PSI-MI_slim is_a: MI:1094 ! genome databases [Term] id: MI:0925 name: observed-ptm def: "Post translational modification observed on a protein in the context of an interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "observed ptm" EXACT PSI-MI-alternate [] synonym: "observed-ptm" EXACT PSI-MI-short [] is_a: MI:0668 ! feature attribute name [Term] id: MI:0926 name: fiash label def: "This fluorescent label is a small ligand membrane-permeant and nonfluorescent until it binds with high affinity and specificity to the tetracysteine domain. Such in situ labeling adds much less mass than does green fluorescent protein and offers greater versatility in attachment sites as well as potential spectroscopic and chemical properties." [PMID:9657724] subset: PSI-MI_slim synonym: "4',5'-bis(1,3,2-dithioarsolan-2-yl)fluorescein " EXACT PSI-MI-alternate [] synonym: "FIAsH label" EXACT PSI-MI-alternate [] is_a: MI:0857 ! fluorescent dye label [Term] id: MI:0927 name: iaedans label def: "IAEDANS is fluorescent tag that bind to cysteines. IAEDANS is the acronyme of (5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid) with free SH groups." [PMID:11052891] subset: PSI-MI_slim synonym: "(5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid) " EXACT PSI-MI-alternate [] synonym: "1,5-IAEDANS" EXACT PSI-MI-alternate [] synonym: "IAEDANS" EXACT PSI-MI-alternate [] is_a: MI:0857 ! fluorescent dye label [Term] id: MI:0928 name: filter trap assay def: "Biomolecules are mixed in a buffer and the resulting mixture is\npassed through a filter. Large\naggregates are retained on the filter and the pariticipants may then be identified." [PMID:10859365] subset: PSI-MI_slim synonym: "filter binding" EXACT [] synonym: "filter retardation assay" RELATED [] synonym: "Filter retention assay" EXACT PSI-MI-alternate [] synonym: "membrane filtration" RELATED [] is_a: MI:0013 ! biophysical is_a: MI:0091 ! chromatography technology [Term] id: MI:0929 name: northern blot def: "A standard procedure to identify RNA fragments containing specific\nsequences. In this procedure RNA fragments are separated by\nelectrophoresis, the fragments are transferred to a membrane and the\nmembrane is incubated with a radio labelled probe that hybridises any\ncomplementary subsequence." [PMID:414220] subset: PSI-MI_slim synonym: "northen" EXACT PSI-MI-alternate [] is_a: MI:0078 ! nucleotide sequence identification [Term] id: MI:0930 name: epistatis def: "An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\n(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes." [PMID:11988766] subset: PSI-MI_slim synonym: "epistatic genetic interaction" EXACT [] is_obsolete: true [Term] id: MI:0931 name: genetic interaction defined by inequality def: "Two genes A and B present an genetic interaction defined by inequality if the phenotypes of the two single mutants a and b, the double mutant ab and the wild-type WT can be measured quantitatively and described relative to each other by an inequality relationship." [PMID:14755292] subset: PSI-MI_slim synonym: "genetic inequality" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0932 name: noninteractive def: "The observation that, when tested, no interaction was observed between two or more genes, for a given phenotype. In other words, the phenotype of the combined perturbations a and b result in the expected phenotype." [PMID:15833125] subset: PSI-MI_slim synonym: "noninteractive genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] synonym: "noninteractive genetic interaction defined by inequality" EXACT [] is_a: MI:0934 ! neutral genetic interaction [Term] id: MI:0933 name: negative genetic interaction def: "An effect in which two genetic perturbations, when combined, result in a phenotype that is more severe/penetrant than expected given the phenotypes of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\nab < E <= wt\nOR\nwt <= E < ab\nwhere 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:14755292] subset: PSI-MI_slim synonym: "negative gen int" EXACT PSI-MI-short [] is_a: MI:0208 ! genetic interaction [Term] id: MI:0934 name: neutral genetic interaction def: "An effect in which the observed phenotype of individual perturbations and/or the double perturbation collectively exhibit values both greater than AND less than wild type (on the same scale). Alternatively, this could describe a scenario in which individual perturbations result in qualitatively different phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\na < wt < b [ab != E]\nOR\nWith respect to two qualitatively different phenotypes, this may be expressed as an inequality as: \n(a != wt AND b != wt AND a != b)\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively different phenotypes." [PMID:14755292] subset: PSI-MI_slim synonym: "neutral gent int" EXACT PSI-MI-short [] is_a: MI:0208 ! genetic interaction [Term] id: MI:0935 name: positive genetic interaction def: "An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than would be expected from the original phenotypes, in effect making the organism more \"wild type\" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: \nE < ab <= wt\nOR\nwt <= ab < E\nwhere 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:14755292] subset: PSI-MI_slim synonym: "positive gent int" EXACT PSI-MI-short [] is_a: MI:0208 ! genetic interaction [Term] id: MI:0936 name: emdb def: "The Electron Microscopy Data Bank (EMDB) contains experimentally determined three-dimensional maps and associated experimental data and files." [PMID:14643225] subset: PSI-MI_slim synonym: "Electron Microscopy Data Bank" EXACT PSI-MI-alternate [] synonym: "eMDB" EXACT PSI-MI-short [] xref: search-url: "www.ebi.ac.uk/pdbe/entry/emdb/${ac}" is_a: MI:0472 ! pdbe [Term] id: MI:0937 name: glu tag def: "This peptide is a 314 to 319 amino acids fragment of the middle T antigen of mouse polymavirus. Glu-Glu epitope peptide." [PMID:8077219] subset: PSI-MI_slim synonym: "glu tag" EXACT PSI-MI-short [] is_a: MI:0507 ! tag [Term] id: MI:0938 name: rheology measurement def: "Characterization of viscoelastic properties of biomolecule solution is used to infer interactions between molecules." [PMID:18445655] subset: PSI-MI_slim synonym: "rheology" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical [Term] id: MI:0939 name: fluorescein label def: "Fluorescence label used to monitor the presence of a protein." [PMID:14755292] subset: PSI-MI_slim synonym: "fluorescein" EXACT PSI-MI-short [] is_a: MI:0857 ! fluorescent dye label [Term] id: MI:0940 name: fluorescein-5-maleimide label def: "Fluorescein-5-maleimide is one of the most popular fluorescent dyes for thiol modifications of proteins at cysteine residues that either are intrinsically present or result from reduction of cystines. Unlike iodoacetamides, maleimides do not react with histidines and methionines under physiological conditions." [PMID:18066077] subset: PSI-MI_slim synonym: "fluor-5-maleimide" EXACT PSI-MI-short [] is_a: MI:0939 ! fluorescein label [Term] id: MI:0941 name: competitor def: "Binds to the bait molecule in competition with other prey molecules, for example at a shared binding site." [PMID:14755292] subset: PSI-MI_slim synonym: "competitor" EXACT PSI-MI-short [] is_a: MI:0500 ! biological role [Term] id: MI:0942 name: uniprot taxonomy def: "Based on NCBO Taxonomy but adapted for UniProt\nhttp://www.uniprot.org/taxonomy/" [PMID:18836194] subset: PSI-MI_slim synonym: "uniprot taxon" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[0-9]+" xref: search-url: "http://www.uniprot.org/taxonomy/${ac}" is_a: MI:0473 ! participant database [Term] id: MI:0943 name: detection by mass spectrometry def: "'Study of interactions by an analytical technique based on measurements of mass-to-charge ratio of charged particles in a mass spectrometer." [PMID:14755292] subset: PSI-MI_slim synonym: "ms interact detect" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical [Term] id: MI:0944 name: mass spectrometry study of hydrogen/deuterium exchange def: "Mass spectroscopy based measurement of the rate and/or extent of the hydrogen/deuterium exchange." [PMID:18948593] subset: PSI-MI_slim synonym: "h1-h2 ms" EXACT PSI-MI-short [] is_a: MI:0943 ! detection by mass spectrometry [Term] id: MI:0945 name: oxidoreductase activity electron transfer reaction def: "An oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GO:GO\:0016491, PMID:14755292] subset: PSI-MI_slim synonym: "redox reaction" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0946 name: miniaturized immunoprecipitation def: "Combines on-chip in-vitro protein synthesis with an in situ microfluidic affinity assay. Co-spotted DNA microarray containing a linear template encoding the proteins is aligned and bonded with a microfluidic device that creates chambers in the array chip. The experiment consists of three main stages: (i) a biotinylated antibody that recognizes the bait protein on a circular area in deposited inside each individual chamber; (ii) proteins are expressed in vitro by transcription and translation of DNA spotted on the chip; (iii) the bait is immobilized on the chamber surface by the antibody and the chamber is washed, retaining only interacting bait-prey pairs." [PMID:19098921] subset: PSI-MI_slim synonym: " protein interaction network generator" EXACT [] synonym: "mIP" EXACT PSI-MI-short [] synonym: "ping" EXACT [] is_a: MI:0019 ! coimmunoprecipitation is_a: MI:0092 ! protein in situ array [Term] id: MI:0947 name: bead aggregation assay def: "Binding of proteins bound to beads leads to a measurable aggregation of the beads." [PMID:19114658] subset: PSI-MI_slim synonym: "bead aggregation" EXACT PSI-MI-short [] is_a: MI:0892 ! solid phase assay [Term] id: MI:0948 name: kinetic conditions def: "A brief description (such as temp, pH) of the conditions under which a kinetic measurment has been performed." [PMID:14755292] subset: PSI-MI_slim synonym: "kinetic_conditions" EXACT PSI-MI-short [] is_a: MI:0664 ! interaction attribute name [Term] id: MI:0949 name: gdp/gtp exchange assay def: "Experiments monitoring\ninteractions of GTP-GDP exchange factors with their cognate GTPases." [PMID:17925023] subset: PSI-MI_slim synonym: "gdp_gtp exchange" EXACT PSI-MI-short [] synonym: "gtp/gdp exchange" EXACT PSI-MI-alternate [] synonym: "guanine nucleotide exchange assay" EXACT PSI-MI-alternate [] is_a: MI:1036 ! nucleotide exchange assay [Term] id: MI:0950 name: trapping mutant def: "Permits the identification of substrates of enzymes by mutating residues, usually in the active site such that the enzyme will bind but not act on its substrate." [PMID:9050838] subset: PSI-MI_slim synonym: "trap-mutant" EXACT PSI-MI-short [] is_a: MI:0505 ! experimental feature [Term] id: MI:0951 name: chain parent sequence reference def: "Reference to the master sequence from which this chain has been derived." [PMID:17925023] subset: PSI-MI_slim synonym: "chain-parent" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0952 name: imex secondary def: "Deprecated IMEx identifiers should be exchanged in IMEx records and stored as cross reference with this qualifier." [PMID:17925023] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0953 name: polymerization def: "Interaction inferred by monitoring polymerization/depolymerization of an interactor" [PMID:19081060] subset: PSI-MI_slim synonym: "polymerization" EXACT [] is_a: MI:0401 ! biochemical [Term] id: MI:0954 name: curation quality def: "An assessment of the depth and extent to which a paper has been curated" [PMID:17893861] subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0955 name: curation depth def: "Assessment of the depth to which a paper has been curated" [PMID:17893861] relationship: part_of MI:0954 ! curation quality [Term] id: MI:0956 name: curation coverage def: "Assessment to the extent of interactions captured in this paper" [PMID:17893861] subset: PSI-MI_slim relationship: part_of MI:0954 ! curation quality [Term] id: MI:0957 name: full coverage def: "All interactions which can be ascribed to an unambiguous identified in this paper have been captured." [PMID:17893861] subset: PSI-MI_slim is_a: MI:0956 ! curation coverage [Term] id: MI:0958 name: partial coverage def: "Not all interactions which can be ascribed to an unambiguous identified in this paper have been captured." [PMID:17893861] subset: PSI-MI_slim is_a: MI:0956 ! curation coverage [Term] id: MI:0959 name: imex curation def: "Paper has been curated to full IMEx specifications" [PMID:17893861] subset: PSI-MI_slim is_a: MI:0955 ! curation depth [Term] id: MI:0960 name: mimix curation def: "Paper has been curated to meet MIMIx specifications" [PMID:17687370] subset: PSI-MI_slim is_a: MI:0955 ! curation depth [Term] id: MI:0961 name: rapid curation def: "Minimal interaction data has been extracted from the paper" [PMID:17687370] subset: PSI-MI_slim is_a: MI:0955 ! curation depth [Term] id: MI:0962 name: strep ii tag def: "The protein of interest is expressed with a StrepII fusion peptide Ser-Ala-Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (SAWSHPQFEK)." [PMID:17571060] subset: PSI-MI_slim synonym: "Strep (II)" EXACT PSI-MI-alternate [] synonym: "Strep II" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0963 name: interactome parallel affinity capture def: "A specific pull down method where the protein of interest (bait) is endogenously expressed with at least two affinity tags (GFP, FLAG or others). The bait is purified in parallel using different purification protocols in contrast to tandem affinity purification (TAP) (publication currently in press)." [PMID:14681455] synonym: "ipac" EXACT PSI-MI-short [] is_a: MI:0096 ! pull down created_by: orchard creation_date: 2009-05-14T10:56:21Z [Term] id: MI:0964 name: infrared spectroscopy def: "Subset of spectroscopy that deals with the infrared region of the electromagnetic spectrum." [PMID:15212548] subset: PSI-MI_slim synonym: "ir spectrometry" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical created_by: orchard creation_date: 2009-10-28T10:55:01Z [Term] id: MI:0965 name: 2d-infrared spectrometry def: "Two-dimensional infrared correlation spectroscopy analysis is the application of 2D correlation analysis on infrared spectra. 2D IR spectroscopy probes molecular structures by means of vibrational frequencies, couplings, and transition dipole angles." [PMID:17502604] subset: PSI-MI_slim synonym: "2d-ir" EXACT PSI-MI-short [] is_a: MI:0964 ! infrared spectroscopy created_by: orchard creation_date: 2009-10-28T11:05:01Z [Term] id: MI:0966 name: ultraviolet-visible spectroscopy def: "Ultraviolet-visible spectroscopy or ultraviolet-visible spectrophotometry (UV-Vis or UV/Vis) involves the spectroscopy of photons in the UV-visible region. This means it uses light in the visible and adjacent (near ultraviolet (UV) and near infrared (NIR)) ranges." [PMID:18799738] synonym: "ultraviolet-visible spectrophotometry" EXACT [] synonym: "uv-vis" EXACT PSI-MI-short [] synonym: "UV/Vis" EXACT [] is_a: MI:0013 ! biophysical created_by: orchard creation_date: 2009-10-28T11:12:27Z [Term] id: MI:0967 name: chembl compound def: "ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets." [PMID:19194660, PMID:24214965] subset: Drugable subset: PSI-MI_slim synonym: "chembl" EXACT [] xref: id-validation-regexp: "[0-9]+" xref: search-url: "http://www.ebi.ac.uk/chembldb/index.php/compound/inspect/${ac}" is_a: MI:2054 ! bioactive entity reference relationship: part_of MI:1349 ! chembl created_by: orchard creation_date: 2009-10-28T11:20:55Z [Term] id: MI:0968 name: biosensor def: "A biosensor is a device for the detection of an analyte that combines a biological component with a physicochemical detector component" [PMID:10872504] subset: PSI-MI_slim is_a: MI:0013 ! biophysical created_by: orchard creation_date: 2009-10-28T11:44:32Z [Term] id: MI:0969 name: bio-layer interferometry def: "BLI is an optical analytical technique that analyzes the interference pattern of white light reflected from two surfaces: a layer of immobilized protein on the biosensor tip, and an internal reference layer" [PMID:19561609] subset: PSI-MI_slim synonym: "bli" EXACT PSI-MI-alternate [] is_a: MI:0968 ! biosensor created_by: orchard creation_date: 2009-10-28T11:48:40Z [Term] id: MI:0970 name: inchi key def: "InChIKeys consist of 14 characters resulting from a hash of the connectivity information of the InChI, followed by a hyphen, followed by 9 characters resulting from a hash of the remaining layers of the InChI, followed by a single character indication the version of InChI used, another hyphen, followed by single checksum character" [PMID:15889163] subset: Drugable synonym: "inchi key" EXACT PSI-MI-short [] is_a: MI:1212 ! checksum is_a: MI:2091 ! structure representation attribute name created_by: orchard creation_date: 2009-10-28T01:13:25Z [Term] id: MI:0971 name: phosphopantetheinylation def: "The posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine." [PMID:19679086] subset: PSI-MI_slim synonym: "p_patetheinylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2009-10-28T01:20:40Z [Term] id: MI:0972 name: phosphopantetheinylase assay def: "Assay of the posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine." [PMID:19346479] synonym: "p_pantethinyl assay" EXACT PSI-MI-short [] synonym: "phosphopantetheinylation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2009-10-28T01:23:19Z [Term] id: MI:0973 name: imex source def: "Databases that contain curated experimental interaction data and exchanging it with other IMEx databases." [PMID:17893861] subset: PSI-MI_slim is_a: MI:0489 ! source database created_by: orchard creation_date: 2009-12-18T10:24:37Z [Term] id: MI:0974 name: innatedb def: "Human and mouse experimentally verified interactions and pathways involved in innate immunity." [PMID:18766178] subset: PSI-MI_slim is_a: MI:0461 ! interaction database is_a: MI:0973 ! imex source created_by: orchard creation_date: 2010-04-09T03:11:54Z [Term] id: MI:0975 name: fc-igg tag def: "A fusion protein tag consisting of a portion of the constant region of IgG." [PMID:11757069] subset: PSI-MI_slim is_a: MI:0240 ! fusion protein created_by: orchard creation_date: 2010-04-21T02:18:04Z [Term] id: MI:0976 name: total internal reflection fluorescence spectroscopy def: "Used to study surface-associated interactions at the molecular level. In this method, the evanescent field from an internally reflected excitation source selectively excites fluorescent molecules on or near a surface." [PMID:9013655] subset: PSI-MI_slim synonym: "tirfs" EXACT PSI-MI-short [] is_a: MI:0051 ! fluorescence technology created_by: orchard creation_date: 2010-04-21T02:30:46Z [Term] id: MI:0977 name: no-imex-export def: "Prevents export of experiment and associated interactions to IMEx" [PMID:17893861] subset: PSI-MI_slim is_a: MI:0665 ! experiment attribute name created_by: orchard creation_date: 2010-04-21T02:49:48Z [Term] id: MI:0978 name: author-name def: "Author given name for a participant, not commonly found in source databases." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0666 ! participant attribute name created_by: orchard creation_date: 2010-04-21T02:55:39Z [Term] id: MI:0979 name: oxidoreductase assay def: "Catalysis of oxido-reductions. The substrate oxidized is regarded as the hydrogen or electron donor. The classification is based on 'donor:acceptor oxidoreductase'. The common name is 'dehydrogenase', wherever this is possible; as an alternative, 'acceptor reductase' can be used. 'Oxidase' is used only where O2 is an acceptor." [PMID:14755292] subset: PSI-MI_slim synonym: "oxidoreduct assay" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-21T03:04:54Z [Term] id: MI:0980 name: tag visualisation by enzyme assay def: "The protein is expressed as a hybrid protein fused to a tag containing an enzyme activity e.g. peroxidase. Subsequence observation or measurement of enzyme activity is used to identify the presence of the molecule in an interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "tag enzyme assay" EXACT PSI-MI-short [] is_a: MI:0866 ! tag visualisation created_by: orchard creation_date: 2010-04-21T03:18:09Z [Term] id: MI:0981 name: tag visualisation by peroxidase activity def: "The protein is expressed as a hybrid protein fused to a tag containing a peroxidase activity. Subsequent observation or measurement of peroxidase activity is used to identify the presence of the molecule in an interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "tag perox activity" EXACT PSI-MI-short [] is_a: MI:0980 ! tag visualisation by enzyme assay created_by: orchard creation_date: 2010-04-21T03:34:14Z [Term] id: MI:0982 name: electrophoretic mobility-based method def: "Any method which relies on the motion of particles relative to a matrix under the influence of an electrical field." [PMID:19517512] subset: PSI-MI_slim synonym: "electrophoresis" EXACT PSI-MI-short [] is_a: MI:0401 ! biochemical created_by: orchard creation_date: 2010-04-26T10:30:36Z [Term] id: MI:0983 name: gemma def: "GEMMA is a method to study protein complexes in solution: a diluted protein sample is transmitted\ninto the gas phase by a charged reduced electrospray process. The generated particles, each\ncontaining one protein molecule with a +1 charge, are separated according to size in a differential\nmobility analyzer and subsequently quantified by a particle counter. In contrast to mass spectrometry,\nthis method is run at atmospheric pressure and measures the diameter of the particle rather than the mass." [PMID:16861739] subset: PSI-MI_slim is_a: MI:0982 ! electrophoretic mobility-based method created_by: orchard creation_date: 2010-04-26T10:36:41Z [Term] id: MI:0984 name: deamination assay def: "The measurement of the removal of an amine group from a molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "aminase assay" EXACT PSI-MI-alternate [] synonym: "deamination" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T10:45:01Z [Term] id: MI:0985 name: deamination reaction def: "The removal of an amine group from a molecule." [PMID:14760721] subset: PSI-MI_slim synonym: "deamination" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2010-04-26T10:49:06Z [Term] id: MI:0986 name: nucleic acid strand elongation reaction def: "The lengthening of a strand of a nucleic acid by the systematic addition of bases by a polymerase." [PMID:159156] subset: PSI-MI_slim synonym: "strand elongation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2010-04-26T10:52:22Z [Term] id: MI:0987 name: rna strand elongation def: "The process by which an RNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent RNA strand." [PMID:14755292] subset: PSI-MI_slim synonym: "rna elongation" EXACT PSI-MI-short [] is_a: MI:0986 ! nucleic acid strand elongation reaction created_by: orchard creation_date: 2010-04-26T11:00:08Z [Term] id: MI:0988 name: strep tag def: "Synthetic peptide consisting of 8 amino acids Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (WSHPQFEK)." [PMID:17571060] subset: PSI-MI_slim is_a: MI:0507 ! tag created_by: orchard creation_date: 2010-04-26T11:07:37Z [Term] id: MI:0989 name: amidase assay def: "The measurement of the addition of an amine group to a molecule." [PMID:14760721] subset: PSI-MI_slim synonym: "amidation" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T11:20:23Z [Term] id: MI:0990 name: cleavage assay def: "The cleavage of a biomolecule either into its component parts or sub-parts." [PMID:14760721] subset: PSI-MI_slim synonym: "cleavage" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T11:27:22Z [Term] id: MI:0991 name: lipoprotein cleavage assay def: "The cleavage of a lipid molecule from a larger biomolecule." [PMID:14760721] subset: PSI-MI_slim is_a: MI:0990 ! cleavage assay created_by: orchard creation_date: 2010-04-26T11:30:12Z [Term] id: MI:0992 name: defarnesylase assay def: "Measures the removal of S-farnesyl-L-cysteined, which is cleaved and returns a C residue." [PMID:14760721] subset: PSI-MI_slim synonym: "defarnesylation assay" EXACT PSI-MI-short [] is_a: MI:0991 ! lipoprotein cleavage assay created_by: orchard creation_date: 2010-04-26T12:27:47Z [Term] id: MI:0993 name: degeranylase assay def: "Measures the removal of S-geranylgeranyl-L-cysteine, which is cleaved and returns a C residue." [PMID:14760721] subset: PSI-MI_slim synonym: "degeranylation assay" EXACT PSI-MI-short [] is_a: MI:0991 ! lipoprotein cleavage assay created_by: orchard creation_date: 2010-04-26T12:36:51Z [Term] id: MI:0994 name: demyristoylase assay def: "measures the removal of N6-myristoyl-L-lysine, which is cleaved and returns a K residue." [PMID:14760721] subset: PSI-MI_slim synonym: "demyristoylation assay" EXACT PSI-MI-short [] is_a: MI:0991 ! lipoprotein cleavage assay created_by: orchard creation_date: 2010-04-26T12:39:30Z [Term] id: MI:0995 name: depalmitoylase assay def: "Measures the removal of S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine, which are cleaved and return C,K,T or S residues." [PMID:14760721] subset: PSI-MI_slim synonym: "depalmitoylation assay" EXACT PSI-MI-short [] is_a: MI:0991 ! lipoprotein cleavage assay created_by: orchard creation_date: 2010-04-26T12:42:00Z [Term] id: MI:0996 name: deformylase assay def: "Measures the removal of N6-formyl-L-lysine, which is cleaved and returns a K residue." [PMID:14760721] subset: PSI-MI_slim synonym: "deformylase reaction" EXACT PSI-MI-short [] synonym: "deformylation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T12:50:38Z [Term] id: MI:0997 name: ubiquitinase assay def: "Measures the reversible reaction that creates a covalent bond between a C-terminus G of ubiquitin and a K residue of the target." [PMID:14760721] subset: PSI-MI_slim synonym: "ubiquitinase assay" EXACT PSI-MI-short [] synonym: "ubiquitination" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T12:54:02Z [Term] id: MI:0998 name: deubiquitinase assay def: "Measures the cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins." [PMID:14760721] subset: PSI-MI_slim synonym: "deubiquinase assay" RELATED [] synonym: "deubiquitinase assay" EXACT PSI-MI-short [] synonym: "deubiquitination" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T12:56:41Z [Term] id: MI:0999 name: formylase assay def: "Measurement of the reaction that can affect K or G residues. Reside is functionalised with a formyl group." [PMID:14760721] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:01:44Z [Term] id: MI:1000 name: hydroxylase assay def: "Measurement of the irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues." [PMID:14760721] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:05:19Z [Term] id: MI:1001 name: lipidase assay def: "The covalent binding of a lipid group to a peptide chain." [PMID:14760721] subset: PSI-MI_slim synonym: "lipidation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:09:49Z [Term] id: MI:1002 name: myristoylase assay def: "Measurement of the irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid." [PMID:14707621] subset: PSI-MI_slim synonym: "myristoylation" RELATED [] is_a: MI:1001 ! lipidase assay created_by: orchard creation_date: 2010-04-26T01:16:11Z [Term] id: MI:1003 name: geranylgeranylase assay def: "Measurement of the attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s)." [PMID:14760721] subset: PSI-MI_slim synonym: "geranylgeranylase" EXACT PSI-MI-short [] synonym: "geranylgeranylation" RELATED [] is_a: MI:1001 ! lipidase assay created_by: orchard creation_date: 2010-04-26T01:20:07Z [Term] id: MI:1004 name: palmitoylase assay def: "Measurement of the covalent attachment of palmitic acid to a protein." [PMID:14760721] subset: PSI-MI_slim synonym: "myristoylation" RELATED [] synonym: "palmitoylase assay" EXACT PSI-MI-short [] is_a: MI:1001 ! lipidase assay created_by: orchard creation_date: 2010-04-26T01:27:50Z [Term] id: MI:1005 name: adp ribosylase assay def: "Measurement of the addition of one or more ADP-ribose moieties to molecules." [PMID:14760721] subset: PSI-MI_slim synonym: "adp ribosylase" EXACT PSI-MI-short [] synonym: "adp ribosylation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:30:24Z [Term] id: MI:1006 name: deglycosylase assay def: "Measurement of the removal of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer." [PMID:14760721] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:34:07Z [Term] id: MI:1007 name: glycosylase assay def: "Measurement of the covalently attachment of glycosyl residues to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer." [PMID:14760721] subset: PSI-MI_slim synonym: "glycosylation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:35:37Z [Term] id: MI:1008 name: sumoylase assay def: "Measurement of the reversible reaction that creates a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target." [PMID:14760721] subset: PSI-MI_slim synonym: "sumoylation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:37:31Z [Term] id: MI:1009 name: desumoylase assay def: "Measurement of the reaction that breaks a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target." [PMID:14760721] subset: PSI-MI_slim synonym: "desumylation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:38:56Z [Term] id: MI:1010 name: neddylase assay def: "Measurement of a reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target." [PMID:14760721] subset: PSI-MI_slim synonym: "neddylation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:41:40Z [Term] id: MI:1011 name: deneddylase assay def: "Measurement of the reaction that breaks a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target." [PMID:14760721] subset: PSI-MI_slim synonym: "deneddylation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:42:49Z [Term] id: MI:1012 name: sbp def: "38 amino acid (MDEKTTGWRGGHWEGLAGELEQLRARLEHHPQGQREP) Streptavidin binding peptide." [PMID:117222181] subset: PSI-MI_slim synonym: "steptavidin binding peptide" RELATED [] is_a: MI:0507 ! tag created_by: orchard creation_date: 2010-04-29T08:42:26Z [Term] id: MI:1013 name: ensemblgenomes def: "Genome browser complementary to Ensembl which extends the search space across a broader taxonomic range.\nhttp://www.ensemblgenomes.org" [PMID:19884133] subset: PSI-MI_slim xref: search-url: "http://ensemblgenomes.org/search/eg/${ac}" is_a: MI:1094 ! genome databases created_by: orchard creation_date: 2010-05-06T08:09:20Z [Term] id: MI:1014 name: string def: "STRING is a database and web resource dedicated to protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins." [PMID:18940858] subset: PSI-MI_slim is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2010-07-15T11:00:57Z [Term] id: MI:1015 name: dictybase def: "dictyBase (http://dictybase.org) is the model organism database for Dictyostelium discoideum. It houses the complete genome sequence, ESTs and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome." [] subset: PSI-MI_slim xref: id-validation-regexp: "DDB_G(0-9){7}" is_a: MI:1094 ! genome databases created_by: orchard creation_date: 2010-07-29T01:19:40Z [Term] id: MI:1016 name: fluorescence recovery after photobleaching def: "Slow rate of FRAP recovery when molecule is bound to another compared to inert, non-binding molecule taken as a measure of an interaction." [PMID:15695095, PMID:17711354] subset: PSI-MI_slim synonym: "frap" EXACT PSI-MI-short [] is_a: MI:0051 ! fluorescence technology created_by: orchard creation_date: 2010-11-11T10:39:37Z [Term] id: MI:1017 name: rna immunoprecipitation def: "Proteins are crosslinked to nucleic acids, for example by the addition of formaldehyde. RNA sequences that cross-link with a given protein are isolated by immunoprecipitation of the protein, and reversal of the cross-linking permits recovery and quantitative analysis of the immunoprecipitated RNA by reverse transcription PCR." [PMID:18265380] subset: PSI-MI_slim synonym: "rip" RELATED [] synonym: "rna-ip" EXACT PSI-MI-short [] is_a: MI:0019 ! coimmunoprecipitation created_by: orchard creation_date: 2010-11-11T10:58:47Z [Term] id: MI:1018 name: deltamass def: "A database of protein post translational modifications. www.abrf.org/index.cfm/dm.home" [PMID:8322616] subset: PSI-MI_slim is_a: MI:0447 ! feature database created_by: orchard creation_date: 2010-11-11T11:04:13Z [Term] id: MI:1019 name: protein phosphatase assay def: "Measures the catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate." [] subset: PSI-MI_slim is_a: MI:0434 ! phosphatase assay created_by: orchard creation_date: 2010-11-11T11:30:47Z [Term] id: MI:1020 name: hilyte fluor 488 def: "A carbonyl-reactive fluorescent labelling dye." [PMID:19795889] subset: PSI-MI_slim synonym: "hilyte 488" EXACT PSI-MI-short [] is_a: MI:0857 ! fluorescent dye label created_by: orchard creation_date: 2010-11-11T11:35:48Z [Term] id: MI:1021 name: qx 520 def: "Nonfluorescent dye, act as a quencher in FRET assays." [] subset: PSI-MI_slim is_a: MI:0373 ! dye label created_by: orchard creation_date: 2010-11-11T11:40:16Z [Term] id: MI:1022 name: field flow fractionation def: "A separation technique where a field is applied to a mixture perpendicular to the mixtures flow. The filed can be graviational, centrifugal, magnetic or a cross flow of fluids." [PMID:959835] subset: PSI-MI_slim is_a: MI:0027 ! cosedimentation created_by: orchard creation_date: 2010-11-11T11:55:40Z [Term] id: MI:1023 name: luminogreen def: "A nonfluorescent, biarsenical derivative of fluorescein. LumioGreen is supplied pre-complexed to EDT, is membrane-permeable, and readily enters the cell." [PMID:19935683] subset: PSI-MI_slim is_a: MI:0373 ! dye label created_by: orchard creation_date: 2010-11-11T12:10:26Z [Term] id: MI:1024 name: scanning electron microscopy def: "A type of electron microscope that images the sample surface by scanning it with a high-energy beam of electrons in a raster scan pattern. The electrons interact with the atoms that make up the sample producing signals that contain information about the sample's surface topography, composition and other properties such as electrical conductivity." [PMID:20463740] subset: PSI-MI_slim synonym: "sem" EXACT PSI-MI-alternate [] is_a: MI:0040 ! electron microscopy created_by: orchard creation_date: 2010-11-11T12:17:54Z [Term] id: MI:1025 name: unimod def: "A database of protein modifications for mass spectrometry. www.unimod.org" [PMID:15174123] is_a: MI:0447 ! feature database created_by: orchard creation_date: 2010-11-11T12:24:10Z [Term] id: MI:1026 name: diphtamidase assay def: "Measurement of a modification that converts an L-histidine residue to diphthamide." [PMID:14760721] subset: PSI-MI_slim synonym: "diphtamidase" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-11-11T12:33:29Z [Term] id: MI:1027 name: diphtamidation reaction def: "A modification that converts an L-histidine residue to diphthamide." [PMID:14760721] subset: PSI-MI_slim synonym: "diphthamidation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2010-11-11T12:36:51Z [Term] id: MI:1028 name: modified chromatin immunoprecipitation def: "Chromatin-bound protein networks isolated using magnetic beads coated with antibodies." [PMID:19106085] subset: PSI-MI_slim synonym: "mch-ip" EXACT PSI-MI-short [] is_a: MI:0402 ! chromatin immunoprecipitation assay created_by: orchard creation_date: 2010-11-11T12:58:52Z [Term] id: MI:1029 name: proteomics of isolated chromatin segments def: "Specific nucleic acid probes are fixed to solid supports (e.g. beads) and act as affinity probes. The molecules associated with the nucleic acid probes can then be isolated and identified." [PMID:19135898] subset: PSI-MI_slim synonym: "pich" EXACT PSI-MI-alternate [] is_a: MI:0402 ! chromatin immunoprecipitation assay created_by: orchard creation_date: 2010-11-11T01:03:21Z [Term] id: MI:1030 name: excimer fluorescence def: "Excimer (excited-dimer) fluorescence is produced by complexes formed by two molecules, at least one of which is in an excited state. It is characterized by a lower energy (i.e. red shift) than fluorescence of a single, non-interacting molecule." [PMID:18480256] subset: PSI-MI_slim synonym: "excimer fluoresc" EXACT PSI-MI-short [] is_a: MI:0051 ! fluorescence technology created_by: orchard creation_date: 2010-11-11T01:15:19Z [Term] id: MI:1031 name: protein folding/unfolding def: "A change in the rate of protein folding/unfolding is taken as a measure of chaperone protein binding." [PMID:19940245] subset: PSI-MI_slim synonym: "protein folding" EXACT PSI-MI-short [] is_a: MI:0400 ! affinity technology created_by: orchard creation_date: 2010-11-11T01:24:11Z [Term] id: MI:1032 name: atto 488 def: "Fluorescent tag - maleimide couples to thiols." [PMID:14760721] subset: PSI-MI_slim synonym: "atto 488 maleimide" EXACT [] synonym: "atto488" RELATED [] is_a: MI:1092 ! atto label created_by: orchard creation_date: 2010-11-11T01:33:13Z [Term] id: MI:1033 name: atto 550 def: "Fluorescent tag - maleimide couples to thiols." [PMID:14760721] subset: PSI-MI_slim synonym: "atto550" RELATED [] is_a: MI:1092 ! atto label created_by: orchard creation_date: 2010-11-11T01:39:43Z [Term] id: MI:1034 name: nuclease assay def: "Measures the cleavage of phosphodiesterase bonds between the nucleotide subunits of nucleic acids." [PMID:14760721] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-11-11T01:43:11Z [Term] id: MI:1035 name: deoxyribonuclease assay def: "Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of DNA." [PMID:14760721] subset: PSI-MI_slim synonym: "deoxyribonuclease" EXACT PSI-MI-short [] is_a: MI:1034 ! nuclease assay created_by: orchard creation_date: 2010-11-11T01:45:29Z [Term] id: MI:1036 name: nucleotide exchange assay def: "Experiments monitoring\ninteractions of nucleotide exchange factors with their cognate nucleotidases." [PMID:14760721] subset: PSI-MI_slim synonym: "nucleotide exchange" EXACT PSI-MI-short [] is_a: MI:0401 ! biochemical created_by: orchard creation_date: 2010-11-11T01:54:00Z [Term] id: MI:1037 name: Split renilla luciferase complementation def: "The N-terminal portion of synthetic renilla luciferase (hrluc) is attached to one protein through the linker peptide (GGGS)2 and C-terminal portion of synthetic renilla luciferase is connected to the second protein through the linker (GGGGS)2. Interaction of the 2 proteins recovers hrluc activity and produces light." [PMID:12705589, PMID:22070901] subset: PSI-MI_slim synonym: "renilla luciferase" EXACT PSI-MI-alternate [] is_a: MI:1203 ! split luciferase complementation created_by: orchard creation_date: 2010-11-11T02:54:08Z [Term] id: MI:1038 name: silicon nanowire field-effect transistor def: "Measures selective electrical response to molecules binding to the immobilised bait." [PMID:20080536] subset: PSI-MI_slim synonym: "nanowire transistor" EXACT PSI-MI-alternate [] is_a: MI:0968 ! biosensor created_by: orchard creation_date: 2010-11-11T03:11:33Z [Term] id: MI:1039 name: c-terminal range def: "The C-terminal region of a sequence, exact coordinates not available." [PMID:14760721] subset: PSI-MI_slim synonym: "c-term range" EXACT PSI-MI-short [] is_a: MI:0333 ! feature range status created_by: orchard creation_date: 2010-11-11T03:20:34Z [Term] id: MI:1040 name: n-terminal range def: "The N-terminal region of a sequence, exact coordinates not available." [PMID:14760721] subset: PSI-MI_slim synonym: "n-term range" EXACT PSI-MI-short [] is_a: MI:0333 ! feature range status created_by: orchard creation_date: 2010-11-11T03:27:57Z [Term] id: MI:1041 name: synonym def: "Alternative name or descriptor for an entity." [PMID:14681455] subset: PSI-MI_slim is_a: MI:0300 ! alias type created_by: orchard creation_date: 2010-12-02T10:26:35Z [Term] id: MI:1042 name: pubmed central def: "PubMed Central is the US National Institute of Health free digital archive of biomedical and life science journals." [PMID:12519941] subset: PSI-MI_slim synonym: "pmc" EXACT PSI-MI-short [] is_a: MI:0445 ! literature database created_by: orchard creation_date: 2010-12-08T01:20:48Z [Term] id: MI:1043 name: flannotator def: "A repository for collecting, storing and and searching the annotation of gene or protein expression patterns in Drosophila melongaster. CPTI (Cambridge Protein Trap Identifier)" [PMID:19126575] subset: PSI-MI_slim xref: id-validation-regexp: "CPTO-[0-9]{6}" is_a: MI:0683 ! sequence database created_by: orchard creation_date: 2011-01-06T01:16:48Z [Term] id: MI:1044 name: rice genome annotation project def: "NSF funded annotation project." [PMID:17145706] subset: PSI-MI_slim synonym: "RGAP" RELATED [] is_a: MI:1094 ! genome databases created_by: orchard creation_date: 2011-02-11T01:33:28Z [Term] id: MI:1045 name: curation content def: "Indicates source, depth and standards by which an entry has been added to a database." [PMID:14755292] subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction created_by: orchard creation_date: 2011-03-11T01:16:55Z [Term] id: MI:1046 name: interacting molecules def: "Defines an interaction by the type of binary molecule pairs it can generates." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1045 ! curation content created_by: orchard creation_date: 2011-03-11T01:19:27Z [Term] id: MI:1047 name: protein-protein def: "Interaction between a protein or peptide and a corresponding protein or peptide." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1046 ! interacting molecules created_by: orchard creation_date: 2011-03-11T01:21:28Z [Term] id: MI:1048 name: smallmolecule-protein def: "Interaction between a small molecule and a corresponding protein or peptide." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1046 ! interacting molecules created_by: orchard creation_date: 2011-03-11T01:22:36Z [Term] id: MI:1049 name: nucleicacid-protein def: "Interaction between a nucleic acid and a corresponding protein or peptide." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1046 ! interacting molecules created_by: orchard creation_date: 2011-03-11T01:23:29Z [Term] id: MI:1050 name: interaction representation def: "Provides an indication of the level of post-processing of experimental data relating to specific binary pairs" [PMID:14755292] subset: PSI-MI_slim is_a: MI:1045 ! curation content created_by: orchard creation_date: 2011-03-11T01:25:29Z [Term] id: MI:1051 name: evidence def: "Binary pair is defined by a single piece of experimental evidence." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1050 ! interaction representation created_by: orchard creation_date: 2011-03-11T01:27:00Z [Term] id: MI:1052 name: clustered def: "Binary pair is defined by multiple pieces of experimental evidence which have been clustered together." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1050 ! interaction representation created_by: orchard creation_date: 2011-03-11T01:28:50Z [Term] id: MI:1053 name: data source def: "The source of the data entered into the database." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1045 ! curation content created_by: orchard creation_date: 2011-03-11T01:32:16Z [Term] id: MI:1054 name: experimentally-observed def: "Data has been directly curated into the database from the paper describing the experimental evidence or by direct submission by the experimenter." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1053 ! data source created_by: orchard creation_date: 2011-03-11T01:33:48Z [Term] id: MI:1055 name: internally-curated def: "Data has been directly curated into this database from the paper describing the experimental evidence" [PMID:14755292] subset: PSI-MI_slim is_a: MI:1053 ! data source created_by: orchard creation_date: 2011-03-11T01:35:12Z [Term] id: MI:1056 name: text-mining def: "The data has been entered into the database following extraction from the literature by a computational process." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1053 ! data source created_by: orchard creation_date: 2011-03-11T01:36:34Z [Term] id: MI:1057 name: predicted def: "The interaction has been predicted using a specific algorithm." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1053 ! data source created_by: orchard creation_date: 2011-03-11T01:37:47Z [Term] id: MI:1058 name: imported def: "The data has been imported into the database form an external resource." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1053 ! data source created_by: orchard creation_date: 2011-03-11T01:39:23Z [Term] id: MI:1059 name: complex expansion def: "The method by which complex n-ary data is expanded into binary data. This may be performed manually on data input, or computationally on data export." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1045 ! curation content created_by: orchard creation_date: 2011-03-11T01:41:16Z [Term] id: MI:1060 name: spoke expansion def: "Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with a single designated molecule, usually the bait." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1059 ! complex expansion created_by: orchard creation_date: 2011-03-11T01:42:35Z [Term] id: MI:1061 name: matrix expansion def: "Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with each other." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1059 ! complex expansion created_by: orchard creation_date: 2011-03-11T01:45:52Z [Term] id: MI:1062 name: bipartite expansion def: "Complex n-ary data has been expanded to binary using the bipartite model. This assumes that all molecules in the complex interact with a single externally designated entity." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1059 ! complex expansion created_by: orchard creation_date: 2011-03-11T01:49:08Z [Term] id: MI:1063 name: consensuspathdb def: "ConsensusPathDB-human integrates functional interaction networks including complex protein-protein, metabolic, signaling and gene regulatory interaction networks in Homo sapiens. Data originate from currently 20 public resources for functional interactions (listed below), as well as interactions that we have curated from literature. Data are integrated in a complementary manner and redundancies are avoided." [PMID:21071422] subset: PSI-MI_slim is_a: MI:1106 ! pathways database created_by: orchard creation_date: 2011-06-21T02:40:16Z [Term] id: MI:1064 name: interaction confidence def: "A method used to derive a numerical or empirical measure of confidence in a particular interaction, or in the identification of the participants in an interaction." [PMID:19420069] subset: PSI-MI_slim synonym: "confidence" EXACT PSI-MI-short [] synonym: "scoring system" EXACT [] relationship: part_of MI:0000 ! molecular interaction created_by: orchard creation_date: 2011-07-05T07:13:57Z [Term] id: MI:1065 name: replication-based confidence def: "Methods based on counting the number of replicates in which an interaction has been observed." [PMID:19420069] subset: PSI-MI_slim synonym: "replication score" EXACT PSI-MI-alternate [] synonym: "replication-based scoring system" RELATED [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T07:22:02Z [Term] id: MI:1066 name: structure-based confidence def: "Confidence score based on similarity to interacting molecules of known structure, presence of known interacting domains etc." [PMID:15044803] subset: PSI-MI_slim synonym: "structure score" EXACT PSI-MI-alternate [] synonym: "structure-based scoring system" EXACT [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T07:38:50Z [Term] id: MI:1067 name: function-based confidence def: "Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO function terms." [PMID:21443973] subset: PSI-MI_slim synonym: "function score" EXACT PSI-MI-short [] synonym: "function-based scoring system" EXACT [] is_a: MI:1064 ! interaction confidence is_a: MI:1221 ! author-based confidence created_by: orchard creation_date: 2011-07-05T07:46:28Z [Term] id: MI:1068 name: location-based confidence def: "Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO component terms or co-occurrence in the same tissues." [PMID:18624398] subset: PSI-MI_slim synonym: "colocation score" EXACT PSI-MI-short [] synonym: "location-based scoring system" EXACT [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T07:52:36Z [Term] id: MI:1069 name: network-based confidence def: "Network-based confidence scoring systems assign confidence based on multiple parameters, potentially shared by interacting proteins e.g. interaction partners, topological parameters, comparison\nwith genetic interactions." [PMID:19010802] subset: PSI-MI_slim synonym: "network score" EXACT PSI-MI-short [] synonym: "network-based scoring system" EXACT PSI-MI-short [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T07:59:13Z [Term] id: MI:1070 name: standard-based confidence def: "Confidence scoring system based on comparison to a 'gold standard' set of known interacting molecules." [PMID:16554755] subset: PSI-MI_slim synonym: "gold standard" RELATED [] synonym: "standard score" EXACT PSI-MI-short [] synonym: "standard-based scoring system" EXACT [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T08:09:46Z [Term] id: MI:1071 name: literature-based confidence def: "Confidence in an interaction is based on co-occurrence of an interacting pair or molecules in the same article, or sentence within an article, usually identified by text-mining." [PMID:18005433] subset: PSI-MI_slim synonym: "literature score" EXACT PSI-MI-short [] synonym: "literature-based scoring system" EXACT [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T08:24:46Z [Term] id: MI:1072 name: method-based confidence def: "The confidence of an interaction is assessed on the number of different methods by which it is observed." [PMID:19420069] subset: PSI-MI_slim synonym: "method score" EXACT PSI-MI-short [] synonym: "method-based scoring system" EXACT [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T08:42:47Z [Term] id: MI:1073 name: statistical-based confidence def: "Confidence in an interaction is based on a measure of the probability of these molecules interacting." [PMID:19420069] subset: PSI-MI_slim synonym: "statistical score" EXACT PSI-MI-short [] synonym: "statistical-based scoring system" EXACT [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T08:50:05Z [Term] id: MI:1074 name: rgs-his tag def: "The protein of interest is expressed as a fusion to a RGS(His)n tag." [PMID:19223579] synonym: "rgs-his" EXACT PSI-MI-short [] is_a: MI:0521 ! his tag created_by: orchard creation_date: 2011-07-05T09:52:28Z [Term] id: MI:1075 name: beilstein def: "The Beilstein database is in the field of organic chemistry, in which compounds are uniquely identified by their Beilstein Registry Number." [PMID:ID\:11604014] subset: PSI-MI_slim synonym: "beilstein" EXACT PSI-MI-short [] is_a: MI:2054 ! bioactive entity reference created_by: orchard creation_date: 2011-07-05T10:03:13Z [Term] id: MI:1076 name: einecs def: "The EINECS database provides general information such as CAS number, EINECS number, Substance Name and Chemical Formula for 100,204 chemical substances. Where available each compound entry is linked to risk and safety phrases and IUCLID and OECD chemical data sheets." [PMID:17125194] subset: PSI-MI_slim synonym: "einecs" EXACT PSI-MI-short [] synonym: "European Inventory of Existing Commercial Chemical Substances " EXACT [] is_a: MI:2054 ! bioactive entity reference created_by: orchard creation_date: 2011-07-05T10:09:35Z [Term] id: MI:1077 name: merck index def: "Comprehensive information on chemicals, drugs, and biologicals." [PMID:17832605] subset: PSI-MI_slim synonym: "merck index" EXACT PSI-MI-short [] is_a: MI:2054 ! bioactive entity reference created_by: orchard creation_date: 2011-07-05T10:15:56Z [Term] id: MI:1078 name: plantgdb def: "PlantGDB develops plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities." [PMID:18063570] subset: PSI-MI_slim synonym: "plantgdb" EXACT PSI-MI-short [] is_a: MI:1094 ! genome databases created_by: orchard creation_date: 2011-07-05T10:27:50Z [Term] id: MI:1079 name: ratmap def: "The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB Genetics at Gothenburg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap." [PMID:15608244] subset: PSI-MI_slim synonym: "ratmap" EXACT PSI-MI-short [] is_a: MI:1094 ! genome databases created_by: orchard creation_date: 2011-07-05T10:32:10Z [Term] id: MI:1080 name: tair def: "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community." [PMID:20521243] subset: PSI-MI_slim synonym: "tair" EXACT PSI-MI-short [] synonym: "The Arabidopsis Information Resource" EXACT [] is_a: MI:1094 ! genome databases created_by: orchard creation_date: 2011-07-05T10:34:26Z [Term] id: MI:1081 name: tigr/jcvi def: "The J. Craig Venter Institute was formed in October 2006 through the merger of several affiliated and legacy organizations including The Institute for Genomic Research (TIGR)." [PMID:18287690] subset: PSI-MI_slim synonym: "J. Craig Venter Institute" EXACT [] synonym: "The Institute for Genomic Research" EXACT PSI-MI-short [] synonym: "tigr/jcvi" EXACT PSI-MI-short [] is_a: MI:1094 ! genome databases created_by: orchard creation_date: 2011-07-05T10:44:11Z [Term] id: MI:1082 name: zfin def: "Extensive information on Danio rerio, including genomics databases, developmental stages, publications and molecular tools." [PMID:21036866] synonym: "The Zebrafish Model Organism Database " EXACT [] synonym: "zfin" EXACT PSI-MI-short [] is_a: MI:1094 ! genome databases created_by: orchard creation_date: 2011-07-05T10:53:21Z [Term] id: MI:1083 name: cog def: "Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain." [PMID:11125040] subset: PSI-MI_slim synonym: "Clusters of Orthologous Groups" EXACT [] synonym: "cogg" EXACT PSI-MI-short [] is_a: MI:0447 ! feature database created_by: orchard creation_date: 2011-07-05T10:59:06Z [Term] id: MI:1084 name: photon donor def: "Any molecule that is able to transfer a photon to another chemical species." [PMID:14755292] subset: PSI-MI_slim synonym: "photon donor" EXACT PSI-MI-short [] is_a: MI:0918 ! donor created_by: orchard creation_date: 2011-07-05T11:03:38Z [Term] id: MI:1085 name: photon acceptor def: "Molecule to which a photon may be transferred from an photon donor." [PMID:14755292] subset: PSI-MI_slim synonym: "photon acceptor" EXACT PSI-MI-short [] is_a: MI:0919 ! acceptor created_by: orchard creation_date: 2011-07-05T11:06:47Z [Term] id: MI:1086 name: equilibrium dialysis def: "Two chambers are separated by a dialysis membrane. The molecular weight cut off\n(MWCO) of this membrane is\nchosen such that it will retain the\nreceptor component of the sample\n(the element which will bind\nthe ligand).\nA known concentration and volume\nof ligand is placed into one of\nthe chambers. The ligand is small\nenough to pass freely through the\nmembrane.\nA known concentration of receptor\nis then placed in the remaining\nchamber in an equivalent volume\nto that placed in the first chamber.\nAs the ligand diffuses across the\nmembrane some of it will bind to\nthe receptor and some will remain\nfree in solution. The higher the\naffinity of the interaction, the higher\nthe concentration of ligand that\nwill be bound at any time." [PMID:21609686] synonym: "equilib. dialysis" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical created_by: orchard creation_date: 2011-07-05T11:12:25Z [Term] id: MI:1087 name: monoclonal antibody blockade def: "Method to block a binding site on a molecule, such as a protein, using a monoclonal antibody to test that the binding site is involved in an interaction with another molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "mab blockade" EXACT PSI-MI-short [] is_a: MI:0400 ! affinity technology is_a: MI:2197 ! probe interaction assay created_by: orchard creation_date: 2011-07-05T11:19:37Z [Term] id: MI:1088 name: phenotype-based detection assay def: "Assays that are used to determine interactions by monitoring, for example activation of a certain pathway when screening for inhibitors of a given receptor." [PMID:14755292] synonym: "phenotype-based" EXACT PSI-MI-short [] is_a: MI:0045 ! experimental interaction detection created_by: orchard creation_date: 2011-07-05T11:24:37Z [Term] id: MI:1089 name: nuclear translocation assay def: "Method to detect interaction by inducing nuclear localization of one participant, which would then pull an interacting participant along with it into the nucleus. As both participants are labeled, the difference in nuclear localization between the induced and non-induced states provides an indication of the interaction between the two molecules." [PMID:21684252] subset: PSI-MI_slim synonym: "nuclear translocation" EXACT PSI-MI-short [] is_a: MI:1088 ! phenotype-based detection assay created_by: orchard creation_date: 2011-07-05T11:27:16Z [Term] id: MI:1090 name: bimane label def: "Bromobimanes are low molecular weight non-fluorescent alkyl halides which react with thiol groups to produce highly fluorescent derivatives. The bimane labels, monobromobimane, dibromobimane, and monobromotrimethylammoniobimane, are derivatives of syn-9,10-dioxabimane:1,5-diazabicyclo[3.3.0]octa-3,6-diene-2,8-dione." [PMID:7378449] subset: PSI-MI_slim synonym: "bimane" EXACT PSI-MI-short [] is_a: MI:0857 ! fluorescent dye label created_by: orchard creation_date: 2011-07-05T12:03:52Z [Term] id: MI:1091 name: publication title def: "Title of the publication." [PMID:14755292] subset: PSI-MI_slim synonym: "title" EXACT PSI-MI-short [] is_a: MI:1093 ! bibliographic attribute name created_by: orchard creation_date: 2011-07-05T12:07:49Z [Term] id: MI:1092 name: atto label def: "Fluorescent dyes - spectral range 500 to 700 nm." [PMID:14755292] synonym: "atto label" EXACT PSI-MI-short [] is_a: MI:0857 ! fluorescent dye label created_by: orchard creation_date: 2011-07-05T12:14:52Z [Term] id: MI:1093 name: bibliographic attribute name def: "Attributes specific to the publication." [PMID:14755292] subset: PSI-MI_slim synonym: "bib attribute" EXACT PSI-MI-short [] synonym: "publication attribute" EXACT [] is_a: MI:0665 ! experiment attribute name created_by: orchard creation_date: 2011-07-05T12:55:21Z [Term] id: MI:1094 name: genome databases def: "Databases which are the responsible for the maintenance and subsequent annotation of one or more genomic sequences." [PMID:14755292] subset: PSI-MI_slim synonym: "genome databases" EXACT PSI-MI-short [] is_a: MI:0683 ! sequence database created_by: orchard creation_date: 2011-07-06T07:57:46Z [Term] id: MI:1095 name: hgnc def: "HGNC is the nomenclature committee responsible for the naming of human genes." [PMID:20929869] synonym: "hgnc" EXACT PSI-MI-short [] synonym: "Human Genome Nomenclature Committee" EXACT PSI-MI-short [] is_a: MI:1109 ! gene database created_by: orchard creation_date: 2011-07-06T08:02:03Z [Term] id: MI:1096 name: protein sequence databases def: "Databases dedicated to the collection and annotation of protein sequences." [PMID:21447597] subset: PSI-MI_slim synonym: "protein seq db" EXACT PSI-MI-short [] is_a: MI:0683 ! sequence database created_by: orchard creation_date: 2011-07-06T08:10:40Z [Term] id: MI:1097 name: uniprot def: "UniProt is a centralized repository of protein sequences with comprehensive coverage and a systematic approach to protein annotation, incorporating, interpreting, integrating and standardizing data from numerous sources and is the most comprehensive catalog of protein sequences and functional annotation." [PMID:21051339] subset: PSI-MI_slim synonym: "uniprot" EXACT PSI-MI-short [] is_a: MI:1096 ! protein sequence databases created_by: orchard creation_date: 2011-07-06T08:14:40Z [Term] id: MI:1098 name: uniprot/swiss-prot def: "UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.\nhttp://www.uniprot.org. UniProtKB/Swiss-Prot is manually curated which means that the information in each entry is annotated and reviewed by a curator" [PMID:14681372, PMID:21447597] subset: PSI-MI_slim synonym: "swiss-prot" EXACT PSI-MI-short [] synonym: "UniProt" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}-PRO_[0-9]{10}" xref: search-url: "http://www.uniprot.org/uniprot/${ac}" is_a: MI:0486 ! uniprot knowledge base created_by: orchard creation_date: 2011-07-06T08:17:34Z [Term] id: MI:1099 name: uniprot/trembl def: "UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.\nhttp://www.uniprot.org. The records in UniProtKB/TrEMBL are automatically generated and are enriched with automatic annotation and classification." [PMID:14681372, PMID:21447597] subset: PSI-MI_slim synonym: "trembl" EXACT PSI-MI-short [] synonym: "UniProt" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}-PRO_[0-9]{10}" xref: search-url: "http://www.uniprot.org/uniprot/${ac}" is_a: MI:0486 ! uniprot knowledge base created_by: orchard creation_date: 2011-07-06T08:20:24Z [Term] id: MI:1100 name: bioactive entity def: "Molecules showing activity in a living system but not encoded by a genomic sequence." [PMID:14760721] synonym: "bioactive entity" EXACT PSI-MI-short [] is_a: MI:0313 ! interactor type created_by: orchard creation_date: 2011-07-06T08:23:48Z [Term] id: MI:1101 name: standard inchi key def: "The Standard InChIKey has five distinct components, a 14-character hash of the basic (Mobile-H) InChI layer, an 8-character hash of the remaining layers (except for the /p segment, which accounts for added or removed protons: it is not hashed at all; the number of protons is encoded at the end of the standard InChIKey.) , a 1 flag character, a 1 version character and the last character is a [de]protonation indicator. The overall length of InChIKey is fixed at 27 characters, including separators (dashes)." [PMID:23343401] subset: PSI-MI_slim is_a: MI:0970 ! inchi key created_by: orchard creation_date: 2014-01-21T10:14:02Z [Term] id: MI:1102 name: mapped-identity def: "Sequence has been computationally remapped following removal or update of the original sequence in the underlying sequence database." [PMID:14760721] synonym: "mapped-identity" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type created_by: orchard creation_date: 2011-07-06T09:07:02Z [Term] id: MI:1103 name: solution state nmr def: "NMR solution state analysis provides useful data regarding the type, quantity and arrangement of different atoms in chemical systems, liquids and solids. Samples are dissolved in deuterated solvents and spectra consist of a series of very sharp\ntransitions, due to averaging of anisotropic NMR interactions\nby rapid random tumbling. Solution-state NMR only requires that the molecule be soluble at sufficient concentration for data collection, but becomes increasingly difficult for biomolecules over 30 kDa so that a practical size limitation is placed on full structure determinations." [PMID:20951674] subset: PSI-MI_slim synonym: "solution nmr" EXACT PSI-MI-short [] synonym: "solution state nmr" EXACT [] is_a: MI:0077 ! nuclear magnetic resonance created_by: orchard creation_date: 2011-07-06T09:16:45Z [Term] id: MI:1104 name: solid state nmr def: "Solid-state NMR (ssNMR) does not require that the sample be soluble or form a crystal, and the approach can be used to study molecules larger than 100 kD. Solid-state NMR spectra are very broad, as the full\neffects of anisotropic or orientation-dependent interactions are observed in the spectrum." [PMID:20951674] subset: PSI-MI_slim synonym: "solid state nmr" EXACT PSI-MI-short [] synonym: "ssnmr" EXACT [] is_a: MI:0077 ! nuclear magnetic resonance created_by: orchard creation_date: 2011-07-06T09:23:11Z [Term] id: MI:1105 name: biocyc def: "BioCyc is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism. (http://biocyc.org/)." [PMID:19850718] subset: PSI-MI_slim synonym: "biocyc" EXACT PSI-MI-short [] is_a: MI:1106 ! pathways database created_by: orchard creation_date: 2011-07-06T09:43:03Z [Term] id: MI:1106 name: pathways database def: "Databases which primarily exist to display biomolecular information in structured pathways. Interactions data can be inferred from the published pathways." [PMID:14755292] subset: PSI-MI_slim synonym: "pathways db" EXACT PSI-MI-short [] is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2011-07-07T02:52:18Z [Term] id: MI:1107 name: pid def: "Curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. It is a collaborative project between the US National Cancer Institute (NCI) and Nature Publishing Group (NPG), and is an open access online resource (http://pid.nci.nih.gov/)." [PMID:18832364] synonym: "pathways interaction database" EXACT [] synonym: "pid" EXACT PSI-MI-short [] is_a: MI:1106 ! pathways database created_by: orchard creation_date: 2011-07-07T03:00:27Z [Term] id: MI:1108 name: biocarta def: "BioCarta, whose core business is in assays and reagents, has also developed a collection of diagrams representing molecular and cellular signal transduction pathways." [PMID:14760721] synonym: "biocarta" EXACT PSI-MI-short [] is_a: MI:1106 ! pathways database created_by: orchard creation_date: 2011-07-07T03:05:55Z [Term] id: MI:1109 name: gene database def: "Primarily nomenclature/cross-reference databases, used by curators to establish a link between a gene and protein ID. In some cases, database records do not contain actual sequence but point to loci on specific reference genomes." [PMID:14755292] subset: PSI-MI_slim synonym: "gene dbs" EXACT PSI-MI-short [] is_a: MI:0473 ! participant database created_by: orchard creation_date: 2011-07-08T08:00:33Z [Term] id: MI:1110 name: predicted interaction def: "Interaction has been predicted by either interologue mapping, by an algorithm or by a computational method." [PMID:14755292] subset: PSI-MI_slim synonym: "predicted" EXACT PSI-MI-short [] is_a: MI:0190 ! interaction type created_by: orchard creation_date: 2011-08-03T11:14:11Z [Term] id: MI:1111 name: two hybrid bait or prey pooling approach def: "Individual baits are mated against pools of preys, or pools of baits are mated against individual preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners." [PMID:11283351, PMID:20946815] subset: PSI-MI_slim is_a: MI:0398 ! two hybrid pooling approach created_by: orchard creation_date: 2011-09-29T03:19:21Z [Term] id: MI:1112 name: two hybrid prey pooling approach def: "Individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners." [PMID:20946815] subset: PSI-MI_slim is_a: MI:1111 ! two hybrid bait or prey pooling approach created_by: orchard creation_date: 2011-09-29T03:21:01Z [Term] id: MI:1113 name: two hybrid bait and prey pooling approach def: "def" [PMID:10655498] subset: PSI-MI_slim is_a: MI:0398 ! two hybrid pooling approach created_by: orchard creation_date: 2011-09-29T03:23:17Z [Term] id: MI:1114 name: virhostnet def: "A database of viral-host interactions." [PMID:18984613] subset: PSI-MI_slim is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2011-10-19T01:28:24Z [Term] id: MI:1115 name: spike def: "SPIKE" [PMID:21097778] subset: PSI-MI_slim synonym: "Signalling Pathways Integrated Knowledge Engine" EXACT [] is_a: MI:1106 ! pathways database created_by: orchard creation_date: 2011-11-09T10:27:04Z [Term] id: MI:1116 name: genemania def: "GeneMANIA predicts interactions based on multiple evidences including physical and genetic interactions, pathways, co-localisation, co-expression and protein domain similarity." [PMID:20576703] subset: PSI-MI_slim is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2011-11-09T02:13:28Z [Term] id: MI:1117 name: topfind def: "TopFIND provides information on protein N- and C-termini. Information of proteases and their substrates is provided." [PMID:21822272] subset: PSI-MI_slim synonym: "Termini-oriented protein function inferred database" EXACT [] is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2011-11-16T11:09:25Z [Term] id: MI:1118 name: enhanced yellow fluorescent protein tag def: "A variation of yellow fluorescent protein derived from eGFP." [PMID:10929120] subset: PSI-MI_slim synonym: "eyfp" EXACT PSI-MI-short [] is_a: MI:0368 ! yellow fluorescent protein tag created_by: orchard creation_date: 2011-11-24T03:17:33Z [Term] id: MI:1119 name: nYFP def: "n-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC)." [PMID:11983170] subset: PSI-MI_slim synonym: "N-terminal part of YFP" RELATED [] is_a: MI:0368 ! yellow fluorescent protein tag is_a: MI:1215 ! bifc tag created_by: orchard creation_date: 2011-11-24T03:30:18Z [Term] id: MI:1120 name: cYFP def: "c-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC)." [PMID:11983170] subset: PSI-MI_slim synonym: "C-terminal part of YFP" RELATED [] is_a: MI:0368 ! yellow fluorescent protein tag is_a: MI:1215 ! bifc tag created_by: orchard creation_date: 2011-11-24T03:43:07Z [Term] id: MI:1121 name: ceYFP def: "c-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC)." [PMID:11983170] subset: PSI-MI_slim synonym: "C-terminal part of EYFP" RELATED [] is_a: MI:1118 ! enhanced yellow fluorescent protein tag created_by: orchard creation_date: 2011-11-24T03:43:30Z [Term] id: MI:1122 name: neYFP def: "n-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC)." [PMID:11983170] subset: PSI-MI_slim synonym: "N-terminal part of EYFP" RELATED [] is_a: MI:1118 ! enhanced yellow fluorescent protein tag created_by: orchard creation_date: 2011-11-24T03:44:40Z [Term] id: MI:1123 name: bindingdb def: "BindingDB is a web-accessible public database of experimentally determined protein-ligand binding affinities for drug discovery. http://BindingDB.org" [PMID:11812264, PMID:11836221, PMID:11987162, PMID:17145705] subset: PSI-MI_slim is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2011-11-28T08:55:26Z [Term] id: MI:1124 name: pathwaycommons def: "Allows the user to browse and search pathways across multiple public pathway databases.\nhttp://www.pathwaycommons.org" [PMID:21071392] subset: PSI-MI_slim synonym: "Pathway Commons" EXACT [] is_a: MI:1106 ! pathways database created_by: orchard creation_date: 2011-11-30T03:04:14Z [Term] id: MI:1125 name: direct binding region def: "The defined region of protein which makes physical contact with the interacting partner." [PMID:14755292] comment: Should normally be used with X-ray crystallography or NMR data. subset: PSI-MI_slim synonym: "direct binding" EXACT PSI-MI-short [] is_a: MI:0442 ! sufficient binding region created_by: orchard creation_date: 2012-01-03T01:10:25Z [Term] id: MI:1126 name: self interaction def: "Intra-molecular interaction between two or more regions of the same molecule." [PMID:14755292] comment: The corresponding experimental role will be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information. subset: PSI-MI_slim is_a: MI:0407 ! direct interaction created_by: orchard creation_date: 2012-01-03T01:19:22Z [Term] id: MI:1127 name: putative self interaction def: "Interaction between two or more regions of possibly the same molecule but it is also possible that the observation is due to an interaction between two identical molecules." [PMID:14755292] comment: The corresponding experimental role should be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information. subset: PSI-MI_slim is_a: MI:0407 ! direct interaction created_by: orchard creation_date: 2012-01-03T01:21:58Z [Term] id: MI:1128 name: mutation disrupting interaction strength def: "Region of a molecule whose mutation or deletion totally disrupts an interaction strength." [PMID:14755292] subset: PSI-MI_slim synonym: "mutation disrupting strength" EXACT PSI-MI-short [] is_a: MI:0573 ! mutation disrupting interaction created_by: orchard creation_date: 2012-01-03T01:36:37Z [Term] id: MI:1129 name: mutation disrupting interaction rate def: "Region of a molecule whose mutation or deletion totally disrupts an interaction rate (in the case of interactions inferred from enzymatic reaction).." [PMID:14755292] subset: PSI-MI_slim synonym: "mutation disrupting rate" EXACT PSI-MI-short [] is_a: MI:0573 ! mutation disrupting interaction created_by: orchard creation_date: 2012-01-03T01:37:43Z [Term] id: MI:1130 name: mutation decreasing interaction rate def: "Region of a molecule whose mutation or deletion decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction)." [PMID:14755292] subset: PSI-MI_slim synonym: "mutation decreasing rate" EXACT PSI-MI-short [] is_a: MI:0119 ! mutation decreasing interaction created_by: orchard creation_date: 2012-01-03T01:38:58Z [Term] id: MI:1131 name: mutation increasing interaction rate def: "Region of a molecule whose mutation or deletion increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction)." [PMID:14577292] subset: PSI-MI_slim synonym: "mutation increasing rate" EXACT PSI-MI-short [] is_a: MI:0382 ! mutation increasing interaction created_by: orchard creation_date: 2012-01-03T01:45:09Z [Term] id: MI:1132 name: mutation increasing interaction strength def: "Region of a molecule whose mutation or deletion increases significantly interaction strength." [PMID:14577292] subset: PSI-MI_slim synonym: "mutation increasing strength" EXACT PSI-MI-short [] is_a: MI:0382 ! mutation increasing interaction created_by: orchard creation_date: 2012-01-03T01:45:42Z [Term] id: MI:1133 name: mutation decreasing interaction strength def: "Region of a molecule whose mutation or deletion decreases significantly interaction strength." [PMID:14755292] subset: PSI-MI_slim synonym: "mutation decreasing strength" EXACT PSI-MI-short [] is_a: MI:0119 ! mutation decreasing interaction created_by: orchard creation_date: 2012-01-03T01:48:40Z [Term] id: MI:1134 name: mcherry fluorescent protein tag def: "mCherry is a red monomer which matures extremely rapidly, making it possible to see results very soon after activating transcription. It is highly photostable and resistant to photobleaching. Excitation maximum: 587 nm. Emission maximum: 610 nm." [] synonym: "mcherry" EXACT PSI-MI-short [] is_a: MI:0732 ! red fluorescent protein tag created_by: orchard creation_date: 2012-01-03T02:53:23Z [Term] id: MI:1135 name: venus fluorescent protein tag def: "Introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L), produced Venus. This mutation dramatically accelerates oxidation of the chromophore, the rate-limiting step in fluorescent protein maturation. Additional mutations were also introduced in order to increase the tolerance of Venus to acidic environments and to reduce the sensitivity to chloride. The absorption and emission spectral peaks are 515 and 528 nanometers, respectively." [PMID:14755292] subset: PSI-MI_slim synonym: "venus" EXACT PSI-MI-short [] is_a: MI:0368 ! yellow fluorescent protein tag created_by: orchard creation_date: 2012-01-03T03:05:01Z [Term] id: MI:1136 name: kusabira-green protein tag def: "Monomeric coral fluorescent reporter protein." [PMID:14755292] subset: PSI-MI_slim synonym: "kusabira-green" EXACT PSI-MI-short [] is_a: MI:0367 ! green fluorescent protein tag created_by: orchard creation_date: 2012-01-03T03:10:28Z [Term] id: MI:1137 name: carboxylation assay def: "The measurement of a the introduction of a carboxylic acid group into a substrate." [PMID:14755292] subset: PSI-MI_slim synonym: "carboxylation assay" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2012-01-03T03:17:56Z [Term] id: MI:1138 name: decarboxylation assay def: "The measurement of a the introduction of a carboxylic acid group into a substrate." [PMID:14755292] subset: PSI-MI_slim synonym: "decarboxxylation assay" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2012-01-03T03:22:04Z [Term] id: MI:1139 name: carboxylation reaction def: "Carboxylation is a posttranslational modification of glutamate residues, to gamma-carboxyglutamate, in proteins." [PMID:14755292] subset: PSI-MI_slim synonym: "carboxylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2012-01-03T03:24:05Z [Term] id: MI:1140 name: decarboxylation reaction def: "Decarboxylation is a chemical reaction that releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases (EC number 4.1.1)." [PMID:14755292] subset: PSI-MI_slim synonym: "decarboxylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2012-01-03T03:31:42Z [Term] id: MI:1141 name: s tag def: "S-tag is the name of an oligopeptide derived from pancreatic ribonuclease A (RNase A). The amino acid sequence of the S-tag is: Lys-Glu-Thr-Ala-Ala-Ala-Lys-Phe-Glu-Arg-Gln-His-Met-Asp-Ser." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0507 ! tag created_by: orchard creation_date: 2012-01-03T03:37:51Z [Term] id: MI:1142 name: aminoacylation assay def: "The measurement of the addition of an aminoacyl group to a compound." [PMID:14755292] subset: PSI-MI_slim synonym: "aminoacylation" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2012-01-03T03:46:46Z [Term] id: MI:1143 name: aminoacylation reaction def: "Aminoacylation is the process of adding an aminoacyl group to a compound." [PMID:14755292] subset: PSI-MI_slim synonym: "aminoacylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2012-01-03T03:49:50Z [Term] id: MI:1144 name: protein a tag visualisation def: "Protein A tag is visualized by interacting with IgG antibodies (or their derivatives) that are specifically recognized by protein A." [PMID:14755292] subset: PSI-MI_slim synonym: "protein a visualisation" EXACT PSI-MI-short [] is_a: MI:0866 ! tag visualisation created_by: orchard creation_date: 2012-01-03T03:54:35Z [Term] id: MI:1145 name: phospholipase assay def: "A phospholipase is an enzyme that hydrolyzes phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2012-01-03T04:04:16Z [Term] id: MI:1146 name: phospholipase reaction def: "Measurement of the hydrolysis of phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2012-01-03T04:08:14Z [Term] id: MI:1147 name: ampylation assay def: "Measurement of AMPylation, the formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino\nacids." [PMID:14755292] subset: PSI-MI_slim synonym: "ampylation assay" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2012-01-03T04:18:27Z [Term] id: MI:1148 name: ampylation reaction def: "AMPylation, previously known as adenylylation, is formation of a\nphosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys\n(RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino\nacids." [PMID:14755292] subset: PSI-MI_slim synonym: "ampylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2012-01-03T04:21:12Z [Term] id: MI:1149 name: cooperative interaction def: "A set of molecular binding events that influence each other either positively or negatively through allostery or pre-assembly. In this context, covalent post-translational modifications are considered as binding events. CV terms that are part of this term allow the description of cooperative interactions using the current PSI-MI schema." [PMID:18641616] subset: PSI-MI_slim synonym: "cooperativity" EXACT [] relationship: part_of MI:0000 ! molecular interaction created_by: orchard creation_date: 2012-06-07T12:21:30Z [Term] id: MI:1150 name: affected interaction def: "For an interaction that has a cooperative effect on a subsequent interaction, this term indicates which subsequent interaction is affected. The affected interaction is identified by referring to its interaction id." [PMID:18641616] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name relationship: part_of MI:1149 ! cooperative interaction created_by: orchard creation_date: 2012-06-07T12:26:42Z [Term] id: MI:1151 name: participant-ref def: "Referring to a previously described interaction as a participant allows the description of ordered assembly of molecular complexes in PSI-MI2.5. When one of the components of the preformed complex has a feature, the participant-ref term indicates on which component this feature is located. The component is identified by referring to its participant id in the previous interaction." [PMID:18641616] subset: PSI-MI_slim is_a: MI:0668 ! feature attribute name created_by: orchard creation_date: 2012-06-07T12:30:48Z [Term] id: MI:1152 name: cooperative effect value def: "This value quantifies the cooperative effect of an interaction on a subsequent interaction. It is the fold change of the affinity or a catalytic parameter of a molecule for one ligand in the absence, versus presence, of a second ligand or a post-translational modification." [PMID:18706817] subset: PSI-MI_slim synonym: "cooperative coupling" EXACT [] is_a: MI:0664 ! interaction attribute name relationship: part_of MI:1149 ! cooperative interaction created_by: orchard creation_date: 2012-06-07T12:35:01Z [Term] id: MI:1153 name: cooperative effect outcome def: "For an interaction that has a cooperative effect on a subsequent interaction, this term indicates whether this effect is positive or negative, i.e. whether the subsequent interaction is augmented or diminished." [PMID:18706817] relationship: part_of MI:1149 ! cooperative interaction created_by: orchard creation_date: 2012-06-07T12:40:41Z [Term] id: MI:1154 name: positive cooperative effect def: "This term specifies that an interaction augments a subsequent interaction." [PMID:18706817] is_a: MI:0664 ! interaction attribute name is_a: MI:1153 ! cooperative effect outcome created_by: orchard creation_date: 2012-06-07T12:42:19Z [Term] id: MI:1155 name: negative cooperative effect def: "This term specifies that an interaction diminishes a subsequent interaction." [PMID:18706817] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:1153 ! cooperative effect outcome created_by: orchard creation_date: 2012-06-07T12:43:48Z [Term] id: MI:1156 name: cooperative mechanism def: "For an interaction that has a cooperative effect on a subsequent interaction, this term indicates the process that mediates this effect." [PMID:18641616] subset: PSI-MI_slim relationship: part_of MI:1149 ! cooperative interaction created_by: orchard creation_date: 2012-06-07T12:46:30Z [Term] id: MI:1157 name: allostery def: "Reciprocal energetic coupling between two binding events at distinct sites on the same molecule. The first binding event alters the binding or catalytic properties of the molecule for the second binding event." [PMID:18641616, PMID:18706817] subset: PSI-MI_slim synonym: "allosteric regulation" EXACT [] is_a: MI:0664 ! interaction attribute name is_a: MI:1156 ! cooperative mechanism created_by: orchard creation_date: 2012-06-07T12:50:20Z [Term] id: MI:1158 name: pre-assembly def: "A non-allosteric mechanism where the strength of an interaction depends on whether or not a particular molecular complex already exists." [PMID:18641616] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:1156 ! cooperative mechanism created_by: orchard creation_date: 2012-06-07T12:52:44Z [Term] id: MI:1159 name: allosteric molecule def: "A molecule whose binding or catalytic properties at one site are altered by allosteric post-translational modification or binding of an allosteric effector at a distinct site. An allosteric molecule is identified by referring to its participant id." [PMID:18706817] subset: PSI-MI_slim is_a: MI:0500 ! biological role is_a: MI:0664 ! interaction attribute name relationship: part_of MI:1149 ! cooperative interaction created_by: orchard creation_date: 2012-06-07T12:55:09Z [Term] id: MI:1160 name: allosteric effector def: "A ligand that elicits an allosteric response upon binding to a target molecule." [PMID:18706817] subset: PSI-MI_slim is_a: MI:0500 ! biological role is_a: MI:0664 ! interaction attribute name relationship: part_of MI:1149 ! cooperative interaction created_by: orchard creation_date: 2012-06-07T12:57:50Z [Term] id: MI:1161 name: allosteric response def: "This term describes the effect of an allosteric binding event. It specifies which properties of the allosteric molecule are altered, i.e. whether the interaction alters either (a) binding or (b) catalytic properties of the allosteric molecule at a site distinct from the allosteric site." [] subset: PSI-MI_slim relationship: part_of MI:1149 ! cooperative interaction created_by: orchard creation_date: 2012-06-07T01:05:17Z [Term] id: MI:1162 name: allosteric k-type response def: "An allosteric response in which the affinity of a molecule is altered." [PMID:18706817] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:1161 ! allosteric response created_by: orchard creation_date: 2012-06-07T01:08:01Z [Term] id: MI:1163 name: allosteric v-type response def: "An allosteric response in which catalysis (kcat or Vmax) of an enzyme is altered." [PMID:18706817] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:1161 ! allosteric response created_by: orchard creation_date: 2012-06-07T01:09:07Z [Term] id: MI:1164 name: allosteric mechanism def: "The process that mediates the allosteric response of a molecule upon allosteric post-translational modification or binding of an allosteric effector." [] relationship: part_of MI:1149 ! cooperative interaction created_by: orchard creation_date: 2012-06-07T01:10:45Z [Term] id: MI:1165 name: allosteric change in structure def: "The allosteric mechanism where changes in the local structure of an allosteric molecule result in altered binding or catalytic properties." [PMID:18706817] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:1164 ! allosteric mechanism created_by: orchard creation_date: 2012-06-07T01:16:20Z [Term] id: MI:1166 name: allosteric change in dynamics def: "The allosteric mechanism where changes in the local dynamics of an allosteric molecule result in altered binding or catalytic properties." [PMID:18706817] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:1164 ! allosteric mechanism created_by: orchard creation_date: 2012-06-07T01:17:54Z [Term] id: MI:1167 name: allostery type def: "This term indicates the chemical relationship between the two ligands whose binding is allosterically coupled." [PMID:18706817] subset: PSI-MI_slim relationship: part_of MI:1149 ! cooperative interaction created_by: orchard creation_date: 2012-06-07T01:19:57Z [Term] id: MI:1168 name: heterotropic allostery def: "The type of allostery that occurs when the two ligands whose binding is allosterically coupled are not chemically identical." [PMID:18706817] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:1167 ! allostery type created_by: orchard creation_date: 2012-06-07T01:21:25Z [Term] id: MI:1169 name: homotropic allostery def: "The type of allostery that occurs when the two ligands whose binding is allosterically coupled are chemically identical." [PMID:18706817] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:1167 ! allostery type created_by: orchard creation_date: 2012-06-07T01:22:35Z [Term] id: MI:1170 name: pre-assembly response def: "This term describes the way in which preformation of a molecular complex has a non-allosteric cooperative effect on subsequent interactions of its components." [PMID:18641616] subset: PSI-MI_slim relationship: part_of MI:1149 ! cooperative interaction created_by: orchard creation_date: 2012-06-07T01:24:42Z [Term] id: MI:1171 name: composite binding site formation def: "The preformation of a complex results in the generation of a continuous binding site that spans more than one component of this complex. The functional binding site does not exist outside the context of the preformed complex." [PMID:18641616] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:1170 ! pre-assembly response created_by: orchard creation_date: 2012-06-07T01:25:50Z [Term] id: MI:1172 name: altered physicochemical compatibility def: "The addition of a PTM to an interaction interface affects the physicochemical compatibility of the binding site with its binding partner. This can either induce or enhance an interaction, or result in inhibition or even abrogation of an interaction. Multisite modification can mediate rheostatic regulation of the interaction." [PMID:22480932, XX:] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:1170 ! pre-assembly response created_by: orchard creation_date: 2012-06-07T01:26:56Z [Term] id: MI:1173 name: binding site hiding def: "The occurrence of overlapping or adjacent, mutually exclusive binding sites promotes competitive binding. When there is a large difference in affinity of the different sites or in local abundance of competitors, binding at one site results in hiding of the second site, thereby precluding it from interacting when the hiding molecule is present." [PMID:22480932] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:1170 ! pre-assembly response created_by: orchard creation_date: 2012-06-07T01:28:07Z [Term] id: MI:1174 name: configurational pre-organization def: "Multivalent ligands form multiple discrete interactions with one or more binding partners. In some cases, An initial binding event can pre-organize other sites for binding. This reduces the degrees of freedom of these sites, thus reducing the entropic costs of their interactions. In addition, the combined strength of multiple interactions increases the enthalpic stability of each interaction (avidity effect). As a result of such effects, interactions of this kind can have a cooperative effect on subsequent interactions." [PMID:18641616] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:1170 ! pre-assembly response created_by: orchard creation_date: 2012-06-07T01:29:13Z [Term] id: MI:1175 name: allosteric post-translational modification def: "A post-translational modification that elicits an allosteric response upon addition to a target molecule. An allosteric post-translational modification is identified by referring to its feature id." [PMID:18706817] subset: PSI-MI_slim synonym: "allosteric ptm" EXACT PSI-MI-short [] is_a: MI:0252 ! biological feature is_a: MI:0664 ! interaction attribute name relationship: part_of MI:1149 ! cooperative interaction created_by: orchard creation_date: 2012-06-07T01:33:16Z [Term] id: MI:1176 name: sequence based prediction of gene regulatory region binding sites def: "Sequence analysis of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur." [PMID:15131651] subset: PSI-MI_slim synonym: "gene regulatory region prediction" RELATED [] synonym: "sequence based prediction of TG regulatory region binding sites for TF " RELATED [] is_a: MI:0101 ! sequence based prediction created_by: orchard creation_date: 2012-06-07T01:40:25Z [Term] id: MI:1177 name: phylogenetic profiling of predicted gene regulatory region binding sites def: "Sequence analysis based on multiple homologous alignments of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur. These methods often also use transcription factor binding motif models." [PMID:12671656] subset: PSI-MI_slim synonym: "gene regulatory region phylogeny" EXACT [] synonym: "phylogenetic footprinting" RELATED [] is_a: MI:0100 ! sequence based phylogenetic profile is_a: MI:1176 ! sequence based prediction of gene regulatory region binding sites created_by: orchard creation_date: 2012-06-07T01:41:59Z [Term] id: MI:1178 name: sequence based prediction of binding of transcription factor to transcribed gene regulatory elements def: "Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict a transcription factor using structural and sequence features of the protein, e.g., by evaluating if the potential transcription factor protein contains a DNA-binding domain that is known to bind to some regulatory elements, or prediction of transcription factor functional domains (DNA binding, transcription factor dimerization, etc.), all based on sequence or structural features of the transcription factor." [PMID:16381970] subset: PSI-MI_slim synonym: "sequence based prediction of binding of TF to TG promoter" EXACT [] synonym: "transcription factor prediction" EXACT [] is_a: MI:0101 ! sequence based prediction created_by: orchard creation_date: 2012-06-07T01:43:57Z [Term] id: MI:1179 name: partial nucleotide sequence identification def: "Identification of a part of a nucleotide sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clone.s" [PMID:14755292] subset: PSI-MI_slim synonym: "partial nucleotide sequence" EXACT PSI-MI-short [] is_a: MI:0078 ! nucleotide sequence identification created_by: orchard creation_date: 2012-06-07T01:47:03Z [Term] id: MI:1180 name: partial DNA sequence identification def: "Identification of a part of a DNA sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones." [PMID:14755292] subset: PSI-MI_slim synonym: "partial dna sequence" EXACT PSI-MI-short [] is_a: MI:1179 ! partial nucleotide sequence identification created_by: orchard creation_date: 2012-06-07T01:52:27Z [Term] id: MI:1181 name: paired end tags sequence identification def: "Paired-end tags (PET) are the short sequences at the 5 prime and 3 prime ends of the DNA fragment of interest, which can be a piece of genomic DNA or cDNA." [PMID:19339662] subset: PSI-MI_slim synonym: "paired end tags" EXACT PSI-MI-short [] is_a: MI:1180 ! partial DNA sequence identification created_by: orchard creation_date: 2012-06-07T01:53:38Z [Term] id: MI:1182 name: full identification by RNA sequencing def: "Sequencing occurs during the course of the experiment. To sequence RNA, the usual method is first to reverse transcribe the sample to generate cDNA fragments." [] subset: PSI-MI_slim is_a: MI:0078 ! nucleotide sequence identification created_by: orchard creation_date: 2012-06-07T02:02:37Z [Term] id: MI:1183 name: nuclease footprinting def: "Binding of a molecule to a strand of nucleic acid protects that region of nucleic acid from the action of a nuclease. The protected region can subsequently be sequenced and the binding site identified." [PMID:7685766] subset: PSI-MI_slim synonym: "nuclease protection" RELATED [] is_a: MI:0605 ! enzymatic footprinting created_by: orchard creation_date: 2012-06-07T02:08:36Z [Term] id: MI:1184 name: dna adenine methyltransferase identification def: "DNA adenine methyltransferase identification is used to map the binding sites of DNA- and chromatin-binding proteins in eukaryotes. DamID identifies binding sites by expressing the proposed DNA-binding protein as a fusion protein with DNA methyltransferase. Binding of the protein of interest to DNA localizes the methyltransferase in the region of the binding site. Adenosine methylation does not occur naturally in eukaryotes and therefore adenine methylation in any region can be concluded to have been caused by the fusion protein, implying the region is located near a binding site." [PMID:10748524] subset: PSI-MI_slim synonym: "DamID" EXACT PSI-MOD-short [] is_a: MI:1313 ! proximity labelling technology created_by: orchard creation_date: 2012-06-07T02:13:03Z [Term] id: MI:1185 name: tag visualisation by dna adenine methyltransferase def: "Proteins of interest are tagged with Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites. The adenine-methylated DNA fragments are isolated by selective polymerase chain reaction amplification and can be identified by microarray hybridization." [PMID:10748524] subset: PSI-MI_slim synonym: "tag DNA methyltransferase" EXACT PSI-MI-short [] is_a: MI:0980 ! tag visualisation by enzyme assay created_by: orchard creation_date: 2012-06-07T02:22:19Z [Term] id: MI:1186 name: dna methyltransferase tag def: "The protein of interest is fused to Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites." [PMID:10748524] subset: PSI-MI_slim is_a: MI:0365 ! enzyme tag created_by: orchard creation_date: 2012-06-07T02:32:02Z [Term] id: MI:1187 name: damip def: "A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N-6-adenine methylation in nearby sites in the genomic DNA. Methylated DNA fragments are enriched with an antibody against N-6-methyladenine and used for further analysis." [PMID:21472695] subset: PSI-MI_slim is_a: MI:1184 ! dna adenine methyltransferase identification created_by: orchard creation_date: 2012-06-07T02:41:40Z [Term] id: MI:1188 name: tag visualisation by mutated dna adenine methyltransferase def: "A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N-6-adenine methylation in nearby sites in the genomic DNA." [] is_a: MI:1185 ! tag visualisation by dna adenine methyltransferase created_by: orchard creation_date: 2012-06-07T02:46:08Z [Term] id: MI:1189 name: methylation interference assay def: "In interference assays, the DNA will be methylated before the binding assay. Protein binding to DNA protects DNA from methylation by dimethylsulphate. If the contact points are methylated, the protein binding is prevented. After isolating the protein-DNA complex, the methylation sites are cleaved by chemical method. As a result, only those regions out of the binding sites will be cleaved. The protein binding region is not methylated; hence, this region is not cleaved. Although the pattern looks like a footprint, the blank region means \"contact points\"." [PMID:21720958] subset: PSI-MI_slim synonym: "contact point analysis" RELATED [] synonym: "methylation interference" EXACT PSI-MI-short [] synonym: "methylation protection assay" RELATED [] is_a: MI:0605 ! enzymatic footprinting created_by: orchard creation_date: 2012-06-07T02:54:00Z [Term] id: MI:1190 name: hydroxy radical footprinting def: "Hydroxyl radicals are created from the Fenton reaction, which involves reducing Fe2+ with H2O2 to form free hydroxyl molecules. These hydroxyl molecules react with the DNA backbone, resulting in a break. Protein bound regions of the DNA are protected." [PMID:3090544] subset: PSI-MI_slim is_a: MI:0602 ! chemical footprinting created_by: orchard creation_date: 2012-06-07T03:10:48Z [Term] id: MI:1191 name: ultraviolet (uv) footprinting def: "Ultraviolet irradiation excites nucleic acids and creates photoreactions, which results in damaged bases in the DNA strand. Protein bound regions of the DNA are protected. UV footprinting technique can detect sequence-specific protein-DNA interactions in vivo. Protein contacts can inhibit of enhance UV photoproduct formation by affecting the ability of DNA to adopt a geometry necessary for the formation of a UV photoproduct. Thus, differences in the strand-breakage patterns of protein-free and protein-bound DNA can be used to detect protein-DNA contacts." [PMID:2842760, PMID:6728031] subset: PSI-MI_slim is_a: MI:0417 ! footprinting created_by: orchard creation_date: 2012-06-07T03:13:02Z [Term] id: MI:1192 name: antisense oligonucleotides def: "This approach is based on the observation that a synthesized nucleic acid that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0255 ! post transcriptional interference created_by: orchard creation_date: 2012-06-07T03:19:22Z [Term] id: MI:1193 name: partial RNA sequence identification def: "Identification of a part of a RNA sequence, usually then related to the full length sequence by alignment." [PMID:14755292] synonym: "partial rna sequence" EXACT PSI-MI-short [] is_a: MI:1179 ! partial nucleotide sequence identification created_by: orchard creation_date: 2012-06-07T03:40:14Z [Term] id: MI:1194 name: reverse transcription pcr def: "Reverse Transcription PCR (RT-PCR) is used for amplifying DNA from RNA. Reverse transcriptase reverse transcribes RNA into cDNA, which is then amplified by PCR." [PMID:12958470] subset: PSI-MI_slim synonym: "reverse PCR" RELATED [] synonym: "RPCR" RELATED [] synonym: "RT-PCR" EXACT PSI-MI-short [] is_a: MI:0088 ! primer specific pcr created_by: orchard creation_date: 2012-06-07T03:47:13Z [Term] id: MI:1195 name: quantitative pcr def: "Quantitative PCR (Q-PCR) is used to measure the quantity of a PCR product (commonly in real-time). It quantitatively measures starting amounts of DNA, cDNA, or RNA." [PMID:12958470] subset: PSI-MI_slim synonym: "q-pcr" EXACT PSI-MI-short [] synonym: "QRT-PCR" RELATED [] synonym: "RQ-PCR" RELATED [] synonym: "RTQ-PCR" RELATED [] is_a: MI:0088 ! primer specific pcr created_by: orchard creation_date: 2012-06-07T03:56:38Z [Term] id: MI:1196 name: quantitative reverse transcription pcr def: "Technique used to measure the quantity of DNA amplified from RNA." [PMID:12958470] subset: PSI-MI_slim synonym: "QRT-PCR" EXACT PSI-MI-short [] synonym: "RTQ-PCR" RELATED [] is_a: MI:1194 ! reverse transcription pcr created_by: orchard creation_date: 2012-06-07T04:04:42Z [Term] id: MI:1197 name: radioimmunoassay def: "To perform a radioimmunoassay, a known quantity of an antigen is made radioactive, frequently by labeling it with gamma-radioactive isotopes of iodine attached to tyrosine. This radiolabeled antigen is then mixed with a known amount of antibody for that antigen, and as a result, the two chemically bind to one another. Then, a sample containing an unknown quantity of that same antigen is added. This causes the unlabeled (or \"cold\") antigen from the serum to compete with the radiolabeled antigen (\"hot\") for antibody binding sites. As the concentration of \"cold\" antigen is increased, more of it binds to the antibody, displacing the radiolabeled variant, and reducing the ratio of antibody-bound radiolabeled antigen to free radiolabeled antigen. The bound antigens are then separated from the unbound ones, and the radioactivity of the free antigen remaining in the supernatant is measured." [PMID:13846364.] synonym: "RIA" EXACT [] is_a: MI:0421 ! identification by antibody created_by: orchard creation_date: 2012-06-07T04:13:30Z [Term] id: MI:1198 name: immunohistochemistry def: "Method using an antibody coupled with some colouring agent to detect a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody." [PMID:16006601] subset: PSI-MI_slim is_a: MI:0422 ! immunostaining created_by: orchard creation_date: 2012-06-07T04:17:12Z [Term] id: MI:1199 name: anti-tag immunohistochemistry def: "Method using an antibody coupled with some colouring agent to detect a tag fused to a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody." [PMID:16006601] subset: PSI-MI_slim is_a: MI:1198 ! immunohistochemistry created_by: orchard creation_date: 2012-06-07T04:21:23Z [Term] id: MI:1200 name: immunocytochemistry def: "Method using an antibody coupled with some colouring agent to detect a specific protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0422 ! immunostaining created_by: orchard creation_date: 2012-06-07T04:22:00Z [Term] id: MI:1201 name: anti-tag immunocytochemistry def: "Method using an antibody coupled with some colouring agent to detect a specific tag fused to a protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1200 ! immunocytochemistry created_by: orchard creation_date: 2012-06-07T04:33:37Z [Term] id: MI:1202 name: one-strep-tag def: "Synthetic peptide tag (SAWSHPQFEK-(GGGS)2-SAWSHPQFEK)" [PMID:19688738] subset: PSI-MI_slim synonym: "" RELATED [] synonym: "twin-strep-tag" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag created_by: orchard creation_date: 2012-06-07T04:44:55Z [Term] id: MI:1203 name: split luciferase complementation def: "Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate." [PMID:20734273] subset: PSI-MI_slim is_a: MI:0090 ! protein complementation assay created_by: orchard creation_date: 2012-06-07T04:56:59Z [Term] id: MI:1204 name: split firefly luciferase complementation def: "Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of firefly (Photinus pyralis) luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate." [PMID:20734273, PMID:22070901] subset: PSI-MI_slim is_a: MI:1203 ! split luciferase complementation created_by: orchard creation_date: 2012-06-07T05:05:36Z [Term] id: MI:1205 name: luciferase tag def: "Luciferase is a generic term for the class of oxidative enzymes used in bioluminescence and is distinct from a photoprotein. Luciferase catalyzes a bioluminescent reaction which requires the substrate luciferin as well as Mg2+ and ATP, produces green light with a wavelength of 562 nm." [] subset: PSI-MI_slim is_a: MI:0240 ! fusion protein created_by: orchard creation_date: 2012-06-07T05:20:20Z [Term] id: MI:1206 name: renilla-n def: "The n-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." [PMID:12705589] subset: PSI-MI_slim synonym: "N-terminal fragment of renilla luciferase" RELATED [] is_a: MI:0896 ! renilla luciferase protein tag is_a: MI:1215 ! bifc tag created_by: orchard creation_date: 2012-06-07T05:26:34Z [Term] id: MI:1207 name: renilla-c def: "The c-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." [PMID:12705589] synonym: "C-terminal fragment of renilla luciferase" EXACT [] is_a: MI:0896 ! renilla luciferase protein tag is_a: MI:1215 ! bifc tag created_by: orchard creation_date: 2012-06-07T05:31:32Z [Term] id: MI:1208 name: firefly luciferase protein tag def: "Firefly luciferase, is an enzyme from beetles (Photinus pyralis) catalyzing the oxidation of the lucifering pigment (reaction with ATP or oxygen) that produces light. Firefly luciferase produces a greenish yellow light in the 550-570nm range." [PMID:22070901] subset: PSI-MI_slim is_a: MI:1205 ! luciferase tag created_by: orchard creation_date: 2012-06-07T05:32:53Z [Term] id: MI:1209 name: firefly-c def: "The c-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." [PMID:22070901] subset: PSI-MI_slim synonym: "C-terminal fragment of firefly luciferase" EXACT [] is_a: MI:1208 ! firefly luciferase protein tag is_a: MI:1215 ! bifc tag created_by: orchard creation_date: 2012-06-07T05:40:04Z [Term] id: MI:1210 name: firefly-n def: "The n-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." [PMID:22070901] subset: PSI-MI_slim synonym: "N-terminal fragment of firefly luciferase" RELATED [] is_a: MI:1208 ! firefly luciferase protein tag is_a: MI:1215 ! bifc tag created_by: orchard creation_date: 2012-06-07T05:41:30Z [Term] id: MI:1211 name: liposome binding assay def: "Lipid binding proteins incubated with liposomes of known lipid content. Mixture is then centrifuged and proteins bound to liposomes separated out." [PMID:14734570] subset: PSI-MI_slim synonym: "liposome centrifugation assay" RELATED [] is_a: MI:0027 ! cosedimentation created_by: orchard creation_date: 2012-06-07T05:51:15Z [Term] id: MI:1212 name: checksum def: "A fixed-size datum calculated (by using a hash function) for a molecular sequence or structure, typically for purposes of error detection or indexing." [PMID:14755292] subset: PSI-MI_slim synonym: "hashsum" RELATED [] is_a: MI:0666 ! participant attribute name created_by: orchard creation_date: 2012-06-07T05:54:41Z [Term] id: MI:1213 name: n-venus def: "N-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays." [PMID:22229727] subset: PSI-MI_slim is_a: MI:1135 ! venus fluorescent protein tag created_by: orchard creation_date: 2012-06-07T06:33:51Z [Term] id: MI:1214 name: c-venus def: "C-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays." [PMID:22229727] subset: PSI-MI_slim is_a: MI:1135 ! venus fluorescent protein tag created_by: orchard creation_date: 2012-06-07T06:39:30Z [Term] id: MI:1215 name: bifc tag def: "Fusion protein which consists of either the N- or C-terminal sequence of a fluorescent or luciferase protein. Binding of the proteins of interest enable the reassembly of the molecule, indicating that an interaction has occured." [PMID:17406412] subset: PSI-MI_slim is_a: MI:0240 ! fusion protein created_by: orchard creation_date: 2012-06-07T07:13:53Z [Term] id: MI:1216 name: cGFP def: "c-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC)." [PMID:17406412] subset: PSI-MI_slim is_a: MI:0367 ! green fluorescent protein tag is_a: MI:1215 ! bifc tag created_by: orchard creation_date: 2012-06-07T07:19:55Z [Term] id: MI:1217 name: nGFP def: "n-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC)." [PMID:17406412] subset: PSI-MI_slim is_a: MI:0367 ! green fluorescent protein tag is_a: MI:1215 ! bifc tag created_by: orchard creation_date: 2012-06-07T07:20:57Z [Term] id: MI:1218 name: chromosome conformation capture assay def: "Chromosome conformation capture,[1] or 3C, is a high-throughput molecular biology technique used to analyze the organization of chromosomes in a cell's natural state. The basic 3C technique consists of cross-linking by addition of formaldehyde followed by addition of a restriction enzyme in excess to the cross-linked DNA, separating the non-cross-linked DNA from the cross-linked chromatin. A intramolecular ligation step using very low concentrations of DNA favors the ligation of relevant DNA fragments with the corresponding junctions instead of the ligation of random fragments. There are two major types of ligation junctions that are over-represented. One is the junction that forms between neighboring DNA fragments due to incomplete digestion, which represents about 20-30% of all junctions. This number is decreased by reducing the cross-linking stringency in the first step. The other type of junctions over-represented in this technique is the junction that forms when one end of the fragment ligates with the other end of the same fragment, and contributes up to 30% of all junctions formed. High temperature then results in the reversal of the previously formed cross-links. The resulting linear DNA fragment has specific restriction ends as well as a central restriction site corresponding to the site of ligation. The pool of these fragments is collectively referred to as the 3C library." [PMID:11847345] subset: PSI-MI_slim synonym: "chip-3c" EXACT PSI-MI-short [] is_a: MI:0402 ! chromatin immunoprecipitation assay created_by: orchard creation_date: 2012-06-07T07:25:28Z [Term] id: MI:1219 name: enzyme-mediated activation of radical sources def: "Enzyme-mediated activation of radical sources is used to identify partners of a given molecule on the cell surface in living cells Activation of the cross-linking reagent arylazide-biotin tag is accomplished by an enzyme, horseradish peroxidase is featured by radical formation of the labelling reagent by horseradish peroxidase (HRP)." [PMID:21214558] subset: PSI-MI_slim synonym: "emars" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical created_by: orchard creation_date: 2012-06-07T07:34:30Z [Term] id: MI:1220 name: tag visualisation by luciferase assay def: "The protein is expressed as a hybrid protein fused to a tag containing a luciferase activity. Subsequence observation or measurement of luciferase activity is used to identify the presence of the molecule in an interaction." [PMID:20609414] subset: PSI-MI_slim synonym: "tag luciferase" EXACT PSI-MI-short [] is_a: MI:0980 ! tag visualisation by enzyme assay created_by: orchard creation_date: 2012-06-11T11:52:57Z [Term] id: MI:1221 name: author-based confidence def: "A score generated by an author, usually only relevant for that particular dataset." [PMID:14755292] subset: PSI-MI_slim synonym: "author score" EXACT PSI-MI-short [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2012-06-11T11:54:23Z [Term] id: MI:1222 name: mbinfo def: "MBInfo is a wiki based, multimedia, educational resource providing up to date reviews on topics relating to mechanobiology (http://www.mechanobio.info/)." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0461 ! interaction database is_a: MI:0973 ! imex source created_by: orchard creation_date: 2012-06-11T12:20:53Z [Term] id: MI:1223 name: ptm decreasing an interaction def: "Post translational modification on a protein observed to decrease the strength or rate of an interaction." [PMID:14744292] subset: PSI-MI_slim synonym: "decreasing-ptm" EXACT PSI-MI-short [] is_a: MI:0925 ! observed-ptm created_by: orchard creation_date: 2012-06-11T12:56:47Z [Term] id: MI:1224 name: ptm increasing an interaction def: "Post translational modification on a protein observed to increase the strength or rate of an interaction." [PMID:14744292] subset: PSI-MI_slim synonym: "increasing-ptm" EXACT PSI-MI-short [] is_a: MI:0925 ! observed-ptm created_by: orchard creation_date: 2012-06-11T12:58:43Z [Term] id: MI:1225 name: ptm disrupting an interaction def: "Post translational modification on a protein observed to disrupt the strength or rate of an interaction." [PMID:14744292] subset: PSI-MI_slim synonym: "disrupting-ptm" EXACT PSI-MI-short [] is_a: MI:0925 ! observed-ptm created_by: orchard creation_date: 2012-06-11T12:59:28Z [Term] id: MI:1226 name: ampylation assay def: "Formation of phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids" [PMID:14755292] subset: PSI-MI_slim synonym: "ampylation" RELATED [] is_obsolete: true created_by: orchard creation_date: 2012-06-11T01:06:07Z [Term] id: MI:1227 name: lap tag def: "Tag encoding green fluorescent protein (GFP) , a TEV cleavage site, and a second purification tag such as S peptide or 6xHis. The tag can therefore be used for both localisation and affinity purification." [PMID:15644491] subset: PSI-MI_slim synonym: "lap tag" EXACT PSI-MI-short [] synonym: "location and purification tag" RELATED [] is_a: MI:0677 ! tandem tag created_by: orchard creation_date: 2012-06-11T01:16:05Z [Term] id: MI:1228 name: pyo tag def: "A polyoma virus-derived (Pyo) epitope tag (amino acids MEYMPME)." [PMID:9371754] subset: PSI-MI_slim is_a: MI:0507 ! tag created_by: orchard creation_date: 2012-08-10T07:28:55Z [Term] id: MI:1229 name: uridylation assay def: "Measures the formation of a phosphodiester or phosphoramide ester of UMP and an amino acid (MOD:01166)." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2012-08-10T07:46:07Z [Term] id: MI:1230 name: uridylation reaction def: "The formation of a phosphodiester or phosphoramide ester of UMP and amino acid (MOD:01166)." [PMID:14755292] subset: PSI-MI_slim synonym: "umpylation" RELATED [] synonym: "uridylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2012-08-10T07:50:08Z [Term] id: MI:1231 name: aminomethylcoumarin label def: "AMC (aminomethylcoumarin ) is a blue fluorescent tag with reactive derivatives that are used as contrasting probes for double- and triple-labeling in immunofluorescence microscopy, arrays and in situ hybridization and can be attached to proteins or small molecules for reaction monitoring." [PMID:14755292] subset: PSI-MI_slim synonym: "AMC label" EXACT PSI-MI-short [] is_a: MI:1328 ! coumarin label created_by: orchard creation_date: 2012-08-10T07:59:18Z [Term] id: MI:1232 name: aggregation assay def: "An interaction between two proteins is inferred from monitoring the effect of the presence of one of them on the aggregation state of the second." [PMID:22179788] subset: PSI-MI_slim synonym: "aggregation" EXACT PSI-MI-short [] is_a: MI:0401 ! biochemical created_by: orchard creation_date: 2012-08-10T08:07:15Z [Term] id: MI:1233 name: resulting-cleavage def: "The cleavage which results due to the action of a proteolytic enzyme on its substrate." [PMID:14755292] comment: Any feature range given should span the cleavage region e.g. 102-103 if the peptide bond between residues 102 and 103 is cut. subset: PSI-MI_slim is_a: MI:0639 ! resulting-ptm created_by: orchard creation_date: 2012-08-10T08:14:45Z [Term] id: MI:1234 name: silac def: "SILAC (Stable Isotope Labeling by Amino acids in Cell culture) can be used to detect features (typically PTMs) required for a given interaction." [PMID:17139335, PMID:18369856] subset: PSI-MI_slim is_a: MI:0659 ! experimental feature detection created_by: orchard creation_date: 2012-08-10T08:45:50Z [Term] id: MI:1235 name: thermal shift binding def: "Ligand binding to a target protein can stabilize a protein's native state, as shown in the increase of the bound protein's melting temperature. The midpoint of the melting curve of a protein will increase in the presence of ligands that bind more tightly to the native state than the unfolded state." [PMID: 22052482] subset: PSI-MI_slim synonym: "thermal shift" EXACT PSI-MI-short [] synonym: "thermshift binding assay" RELATED [] is_a: MI:0013 ! biophysical created_by: orchard creation_date: 2012-08-10T08:52:14Z [Term] id: MI:1236 name: proline isomerase assay def: "Measurment of the conversion between cis- and trans- peptide bonds formed by the amine group of a proline. Peptide bonds to proline, and to other N-substituted amino acids (such as sarcosine), are able to populate both the cis and trans isomers the cis and trans isomers of the X-Pro peptide bond (where X represents any amino acid) both experience steric clashes with the neighboring substitution and are nearly equal energetically. Hence, the fraction of X-Pro peptide bonds in the cis isomer under unstrained conditions ranges from 10-40%; the fraction depends slightly on the preceding amino acid, with aromatic residues favoring the cis isomer slightly." [PMID:9344417] subset: PSI-MI_slim is_a: MI:1249 ! isomerase assay created_by: orchard creation_date: 2012-08-10T08:56:38Z [Term] id: MI:1237 name: proline isomerization reaction def: "The conversion between cis- and trans- peptide bonds formed by the amine group of a proline." [PMID:9344417] subset: PSI-MI_slim is_a: MI:1250 ! isomerase reaction created_by: orchard creation_date: 2012-08-10T09:02:28Z [Term] id: MI:1238 name: mass spectrometry studies of subunit exchange def: "Heavy/light isotope-labelled subunits are prepared and allowed to form their respective mature oligomeric structure. Oligomers are then mixed and subunit exchange is monitored, usually by electrospray ionisation-ion mobility spectrometry-mass spectrometry." [PMID:20351246] subset: PSI-MI_slim synonym: "ms subunit exchange" EXACT PSI-MI-short [] is_a: MI:0069 ! mass spectrometry studies of complexes created_by: orchard creation_date: 2012-08-10T09:11:36Z [Term] id: MI:1239 name: amino-acid variant def: "A naturally-occuring amino-acid variation to the reference sequence, including polymorphisms, variations between strains, isolates or cultivars, disease-associated mutations and RNA editing events." [PMID:18175334] subset: PSI-MI_slim synonym: "SAP" RELATED [] synonym: "single amino-acid polymorphism" RELATED [] is_a: MI:1241 ! variant created_by: orchard creation_date: 2012-08-10T09:20:55Z [Term] id: MI:1240 name: disease causing amino-acid variant def: "A naturally-occuring amino-acid variation to the reference sequence which results in the organism developing, or becoming susceptible to a particular disease condition." [PMID:18175334] synonym: "disease aa variant" EXACT PSI-MI-short [] synonym: "disease sap" RELATED [] synonym: "disease single amino acid polymorphism" RELATED [] is_a: MI:1239 ! amino-acid variant created_by: orchard creation_date: 2012-08-10T09:28:06Z [Term] id: MI:1241 name: variant def: "A natural change in a sequence or structure in comparison to a reference entity." [] is_a: MI:0252 ! biological feature created_by: orchard creation_date: 2012-08-10T09:32:29Z [Term] id: MI:1242 name: fc-igg1 def: "A fusion protein tag consisting of a portion of the constant region of IgG1." [PMID:11757069] subset: PSI-MI_slim is_a: MI:0975 ! fc-igg tag created_by: orchard creation_date: 2012-08-10T10:10:25Z [Term] id: MI:1243 name: fc-igg2 def: "A fusion protein tag consisting of a portion of the constant region of IgG2." [PMID:11757069] subset: PSI-MI_slim is_a: MI:0975 ! fc-igg tag created_by: orchard creation_date: 2012-08-10T10:14:13Z [Term] id: MI:1244 name: mkate2 def: "Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively." [PMID:17721542] subset: PSI-MI_slim is_a: MI:0732 ! red fluorescent protein tag created_by: orchard creation_date: 2012-08-10T11:22:13Z [Term] id: MI:1245 name: mkate def: "Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively." [PMID:17721542] subset: PSI-MI_slim synonym: "TagFP635" RELATED [] is_a: MI:0732 ! red fluorescent protein tag created_by: orchard creation_date: 2012-08-10T11:48:12Z [Term] id: MI:1246 name: ion mobility mass spectrometry of complexes def: "IM-MS analysis is performed by first ionizing the protein complex of interest followed by ion mobility separation according to their cross-section-to-charge (Q/z) ratio. After separation, ions are sampled by a mass spectrometer and analyzed according to their mass-to-charge (m/z) ratio. Combined knowledge of both Q/z and m/z can be used to infer the size and shape of the complex." [PMID:18600219] subset: PSI-MI_slim synonym: "iM-MS" RELATED [] synonym: "ion mobility mass spec" EXACT PSI-MI-short [] is_a: MI:0069 ! mass spectrometry studies of complexes created_by: orchard creation_date: 2012-08-10T11:56:05Z [Term] id: MI:1247 name: microscale thermophoresis def: "Measurement of the directed movement of particles in a microscopic temperature gradient. Any change of the hydration shell of biomolecules due to changes in their structure/conformation results in a relative change of movement along the temperature gradient and is used to determine binding affinities, binding kinetics and activity kinetics. Events such as the phosphorylation of a protein or the binding of small molecules to a target can be monitored." [PMID: 17164337] subset: PSI-MI_slim synonym: "mst" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical created_by: orchard creation_date: 2012-08-10T12:20:37Z [Term] id: MI:1248 name: bodipy label def: "Composed of dipyrromethene complexed with a disubstituted boron atom, typically a BF2 unit. Notable for their uniquely small Stokes shift, high, environment-independent fluorescence quantum yields." [PMID:19067126] subset: PSI-MI_slim synonym: "4,4-difluoro-4-bora-3a,4a-diaza-s-indacene" RELATED [] synonym: "boron-dipyrromethene label" RELATED [] is_a: MI:0857 ! fluorescent dye label created_by: orchard creation_date: 2012-08-10T12:34:54Z [Term] id: MI:1249 name: isomerase assay def: "Measurement of the catalysis of the structural rearrangement of isomers." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2012-08-10T12:45:27Z [Term] id: MI:1250 name: isomerase reaction def: "The catalysis of the structural rearrangement of isomers." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2012-08-10T12:51:00Z [Term] id: MI:1251 name: methylmalonyl-CoA isomerase reaction def: "The catalysis of the conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1250 ! isomerase reaction created_by: orchard creation_date: 2012-08-10T01:23:35Z [Term] id: MI:1252 name: methylmalonyl-CoA isomerase asf say def: "The catalysis othe conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2" [PMID:147292] subset: PSI-MI_slim is_a: MI:1249 ! isomerase assay created_by: orchard creation_date: 2012-08-10T01:29:23Z [Term] id: MI:1253 name: atto 532 def: "Fluorescent tag - maleimide couples to thiols." [PMID:14760721] subset: PSI-MI_slim synonym: "atto 532 maleimide" EXACT [] synonym: "atto532" RELATED [] is_a: MI:1092 ! atto label created_by: orchard creation_date: 2012-08-10T01:49:01Z [Term] id: MI:1254 name: atto 647 def: "Fluorescent tag - maleimide couples to thiols." [PMID:14760721] subset: PSI-MI_slim synonym: "atto 647 maleimide" EXACT [] synonym: "atto647" RELATED [] is_a: MI:1092 ! atto label created_by: orchard creation_date: 2012-08-10T01:51:00Z [Term] id: MI:1255 name: stilbene label def: "1,2-Diphenylethene" [PMID:16287229] subset: PSI-MI_slim is_a: MI:0857 ! fluorescent dye label created_by: orchard creation_date: 2012-08-10T01:56:28Z [Term] id: MI:1256 name: luminscent dye label def: "Luminescent dyes such as cyanines,commonly used for DNA labelling." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0373 ! dye label created_by: orchard creation_date: 2012-08-10T02:18:02Z [Term] id: MI:1257 name: rhodamine label def: "Rhodamines are supplements to fluoresceins, as they offer longer wavelength emission maxima and provide opportunities for multicolor labeling or staining." [PMID:12622145] subset: PSI-MI_slim is_a: MI:0857 ! fluorescent dye label created_by: orchard creation_date: 2012-08-10T02:39:00Z [Term] id: MI:1258 name: tetramethyl rhodamine label def: "Tetramethyl rhodamine - a derivative of rhodamine." [PMID:12622145] subset: PSI-MI_slim is_a: MI:1257 ! rhodamine label created_by: orchard creation_date: 2012-08-10T02:44:52Z [Term] id: MI:1259 name: acrylodan label def: "The thiol reactive acrylodan (6-acryloyl-2-dimethylaminonaphthalene) generally reacts with thiols more slowly than iodoacetamides or maleimides, but does form very strong thioether bonds that are expected to remain stable under conditions required for complete amino acid analysis. The fluorescence emission peak and intensity of these adducts are particularly sensitive to conformational changes or ligand binding." [PMID:12622145] subset: PSI-MI_slim synonym: "6-acryloyl-2-dimethylaminonaphthalene" RELATED [] is_a: MI:0857 ! fluorescent dye label created_by: orchard creation_date: 2012-08-10T02:55:26Z [Term] id: MI:1260 name: pyrene label def: "Pyrene is a polycyclic aromatic hydrocarbon (PAH) consisting of four fused benzene rings, resulting in a flat aromatic system. The chemical formula is C16H10. Its derivatives are valuable molecular probes via fluorescence spectroscopy, having a high quantum yield and lifetime." [PMID:12622145] is_a: MI:0857 ! fluorescent dye label created_by: orchard creation_date: 2012-08-10T03:09:54Z [Term] id: MI:1261 name: oregon green label def: "Oregon Green 488 and Oregon Green 514 dyes are fluorinated analogs of fluoresceins" [PMID:12622145] subset: PSI-MI_slim is_a: MI:0939 ! fluorescein label created_by: orchard creation_date: 2012-08-10T03:17:05Z [Term] id: MI:1262 name: iid def: "Interologous Interaction Database is an on-line database of known and predicted mammalian and eukaryotic protein-protein interactions." [PMID:19850753] subset: PSI-MI_slim synonym: "i2d" EXACT PSI-MI-alternate [] synonym: "Interologous Interaction Database" EXACT PSI-MI-alternate [] xref: url:http\://iid.ophid.utoronto.ca/iid/ is_a: MI:0461 ! interaction database is_a: MI:0973 ! imex source created_by: orchard creation_date: 2012-10-22T02:57:59Z [Term] id: MI:1263 name: molecular connections def: "Molecular Connections Private Limited is an in silico discovery Services Company with expertise in drug-discovery, informatics and information technology. They perform pro bono work for the IMEx Consortium. http://www.molecularconnections.com" [PMID:22453911] subset: PSI-MI_slim synonym: "MolCon" RELATED [] is_a: MI:0461 ! interaction database is_a: MI:0973 ! imex source created_by: orchard creation_date: 2012-10-22T03:03:01Z [Term] id: MI:1264 name: ntnu def: "Norwegian University of Science and Technology. www.ntnu.no/home." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0489 ! source database created_by: orchard creation_date: 2012-10-22T03:15:27Z [Term] id: MI:1265 name: ubiquitin reconstruction tag def: "In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety (residues 35-76) and an N-terminal ubiquitin moiety (residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases." [PMID:9560251] subset: PSI-MI_slim is_a: MI:0240 ! fusion protein created_by: orchard creation_date: 2012-10-24T11:08:40Z [Term] id: MI:1266 name: cub def: "A C-terminal ubiquitin moiety (cub, residues 35-76) plus a transcription factor that can be cleaved off by ubiquitin specific proteases. Regarded as attached to the bait molecules in ubiquitin reconstruction assays." [PMID:9560251] subset: PSI-MI_slim synonym: "c-terminal ubiquitin tag" RELATED [] is_a: MI:1265 ! ubiquitin reconstruction tag created_by: orchard creation_date: 2012-10-24T11:10:19Z [Term] id: MI:1267 name: nub def: "N-terminal ubiquitin moiety (nub, residues 1-34)." [PMID:9560251] subset: PSI-MI_slim synonym: "N-terminal ubiquitin tag" RELATED [] is_a: MI:1265 ! ubiquitin reconstruction tag created_by: orchard creation_date: 2012-10-24T11:12:47Z [Term] id: MI:1268 name: nubg def: "N-terminal ubiquitin moiety (residues 1-34) containing a Ile13Gly mutation." [PMID:9560251] subset: PSI-MI_slim synonym: "Ile13Gly N-terminal ubiquitin tag" RELATED [] is_a: MI:1267 ! nub created_by: orchard creation_date: 2012-10-24T11:31:11Z [Term] id: MI:1269 name: duplicated protein def: "An identical protein sequence is coded for by the multiple genes within the same organism. These proteins may previously be merged into a single entry by UniProt and subsequently demerged." [PMID:21051339] subset: PSI-MI_slim is_a: MI:1341 ! set member created_by: orchard creation_date: 2012-11-28T03:23:28Z [Term] id: MI:1270 name: xpress tag def: "Contains a polyhistidine sequence, the Xpress epitope (part of bacteriophage T7 gene 10 protein) and an enterokinase cleavage site. Anti-Xpress antibodies recognise the Xpress epitope sequence found in this leader peptide. Asp-Leu-Tyr-Asp-Asp-Asp-Asp-Lys." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0507 ! tag created_by: orchard creation_date: 2013-05-30T08:29:27Z [Term] id: MI:1271 name: enhancement def: "An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation to a severity/penetrance beyond (further from wild type) that expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\nab < E < wt\nOR\nwt < E < ab\nwhere 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim synonym: "Aggravating interaction" RELATED [] is_a: MI:0933 ! negative genetic interaction created_by: orchard creation_date: 2013-06-05T19:12:17Z [Term] id: MI:1272 name: positive epistasis def: "An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in the same direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\n((a* < b < wt) OR (wt < b < a*)) AND (ab = a OR ab = b)\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:0797 ! epistasis is_a: MI:0935 ! positive genetic interaction created_by: orchard creation_date: 2013-06-05T20:05:15Z [Term] id: MI:1273 name: maximal epistasis def: "An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\nab = a* < b < wt\nOR\nwt < b < a* = ab\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [:, PMID:15833125] subset: PSI-MI_slim is_a: MI:1272 ! positive epistasis is_a: MI:1284 ! quantitative epistasis created_by: orchard creation_date: 2013-06-05T20:11:27Z [Term] id: MI:1274 name: minimal epistasis def: "An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the least severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\na* < ab = b < wt\nOR\nwt < b = ab < a*\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:1272 ! positive epistasis is_a: MI:1282 ! mutual suppression (partial) is_a: MI:1284 ! quantitative epistasis created_by: orchard creation_date: 2013-06-05T20:13:14Z [Term] id: MI:1275 name: neutral epistasis def: "An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are EITHER traits measured on the same quantitative scale but each significantly deviating, in opposite directions, from wild type, OR completely (qualitatively) different phenotypes), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\n(a < wt < b) AND (ab = a OR ab = b)\nOR\n(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b)\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value, and 'a != b' indicates qualitatively different phenotypes." [PMID:15833125] subset: PSI-MI_slim is_a: MI:0797 ! epistasis is_a: MI:0934 ! neutral genetic interaction created_by: orchard creation_date: 2013-06-05T20:22:53Z [Term] id: MI:1276 name: opposing epistasis def: "An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\n(a < wt < b) AND (ab = a OR ab = b) \nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:1275 ! neutral epistasis created_by: orchard creation_date: 2013-06-05T20:25:26Z [Term] id: MI:1277 name: qualitative epistasis def: "An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits that cannot be measured on the same scale and, hence, qualitatively different), and the resulting phenotype of their combination is equal to that of only one of the perturbations. This may be expressed as an inequality as:\n(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) \nwhere 'a' and 'b' are the observed phenotypes of the individual perturbations, 'ab' is the observed phenotype of the double perturbation, 'wt' is the wild type phenotype and 'a != b' indicates qualitatively different phenotypes." [PMID:15833125] subset: PSI-MI_slim is_a: MI:1275 ! neutral epistasis created_by: orchard creation_date: 2013-06-05T20:26:38Z [Term] id: MI:1278 name: mutual enhancement def: "An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is more severe/penetrant (further from wild type) than expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\nab < a* <= b < wt [E = a*]\nOR\nwt < b <= a* < ab [E = a*]\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:1271 ! enhancement created_by: orchard creation_date: 2013-06-05T20:31:30Z [Term] id: MI:1279 name: unilateral enhancement def: "An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation (which, on its own, has no effect on the phenotype in question) to a severity/penetrance beyond (further from wild type) that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\nab < a < b = wt [E = a]\nOR\nwt = b < a < ab [E = a]\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125, XX:] subset: PSI-MI_slim is_a: MI:1271 ! enhancement created_by: orchard creation_date: 2013-06-05T20:33:13Z [Term] id: MI:1280 name: mutual suppression def: "An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\n(a* <= b < wt) AND (a* < ab <= wt) [E = a*]\nOR\n(wt < b <= a*) AND (wt <= ab < a*) [E = a*]\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125, XX:] subset: PSI-MI_slim is_a: MI:0796 ! suppression created_by: orchard creation_date: 2013-06-05T20:35:53Z [Term] id: MI:1281 name: mutual suppression (complete) def: "An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting combination is wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\na* <= b < ab = wt\nOR\nwt = ab < b <= a*\nOR\na < wt = ab < b\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:1280 ! mutual suppression created_by: orchard creation_date: 2013-06-05T20:37:41Z [Term] id: MI:1282 name: mutual suppression (partial) def: "An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected, but not wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\n(a* <= b < wt) AND (a* < ab < wt) [E = a*]\nOR\n(wt < b <= a*) AND (wt < ab < a*) [E = a*]\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:1280 ! mutual suppression created_by: orchard creation_date: 2013-06-05T20:39:12Z [Term] id: MI:1283 name: suppression-enhancement def: "An effect in which individual perturbations of different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination has a phenotype more severe/penetrant than the least severe/penetrant and less severe/penetrant than the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\na* < ab < b < wt [E = a*]\nOR\nwt < b < ab < a* [E = a*]\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:1282 ! mutual suppression (partial) created_by: orchard creation_date: 2013-06-05T20:43:52Z [Term] id: MI:1284 name: quantitative epistasis def: "An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in any direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\n(a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) \nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates quantitatively different phenotypes." [PMID:15833125] subset: PSI-MI_slim is_a: MI:0797 ! epistasis created_by: orchard creation_date: 2013-06-05T20:47:35Z [Term] id: MI:1285 name: opposing epistasis def: "An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\n(a < wt < b) AND (ab = a OR ab = b) \nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:1284 ! quantitative epistasis created_by: orchard creation_date: 2013-06-05T20:51:51Z [Term] id: MI:1286 name: over-suppression def: "An effect in which the observed phenotype of a double perturbation is opposite (relative to the wild type phenotype) to that which is expected upon the double perturbation. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\nab < wt < E\nOR\nE < wt < ab\nwhere 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:0934 ! neutral genetic interaction created_by: orchard creation_date: 2013-06-05T21:04:18Z [Term] id: MI:1287 name: mutual over-suppression def: "An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is opposite (relative to wild type) to that expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\na* <= b < wt < ab [E = a*]\nOR\nab < wt < b <= a* [E = a*]\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:1286 ! over-suppression created_by: orchard creation_date: 2013-06-05T21:06:09Z [Term] id: MI:1288 name: over-suppression-enhancement def: "An effect in which two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is more severe than the phenotype observed with the same directionality. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\na < wt < b < ab\nOR\nab < a < wt < b\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:0934 ! neutral genetic interaction created_by: orchard creation_date: 2013-06-05T21:11:03Z [Term] id: MI:1289 name: phenotype bias def: "An effect when two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is intermediate to the individual mutant phenotypes, but greater or less than wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\n(a < wt < b) AND (a < ab < b) AND (ab != wt)\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:0934 ! neutral genetic interaction created_by: orchard creation_date: 2013-06-05T21:15:34Z [Term] id: MI:1290 name: suppression (complete) def: "An effect in which the perturbation of one gene results in complete suppression (to wild type) of the mutant phenotype caused by perturbation of another gene. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\nwt = ab != a = E\nwhere 'a' is the observed phenotype values of an individual perturbation, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:0796 ! suppression created_by: orchard creation_date: 2013-06-05T21:34:57Z [Term] id: MI:1291 name: suppression (partial) def: "An effect in which the perturbation of one gene results in the amelioration or lessening of the severity/penetrance of a mutant phenotype caused by perturbation of another gene, in effect making the organism more, but not completely, \"wild type\" in character with regards to the phenotype in question. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\na* < ab < wt [E = a*]\nOR\nwt < ab < a* [E = a*]\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:0796 ! suppression created_by: orchard creation_date: 2013-06-05T21:36:07Z [Term] id: MI:1292 name: unilateral suppression def: "An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more \"wild type\" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\na < ab <= b = wt [E = a]\nOR\nwt = b <= ab < a [E = a]\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:0796 ! suppression created_by: orchard creation_date: 2013-06-05T21:37:28Z [Term] id: MI:1293 name: unilateral suppression (complete) def: "An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the complete suppression (to wild type) of the mutant phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\na < ab = b = wt [E = a]\nOR\nwt = b = ab < a [E = a]\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:1292 ! unilateral suppression created_by: orchard creation_date: 2013-06-05T21:38:36Z [Term] id: MI:1294 name: unilateral suppression (partial) def: "An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more, but not completely, \"wild type\" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\na < ab < b = wt [E = a]\nOR\nwt = b < ab < a [E = a]\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:1292 ! unilateral suppression created_by: orchard creation_date: 2013-06-05T21:39:32Z [Term] id: MI:1295 name: unilateral over-suppression def: "An effect in which the perturbation of one gene (which has no individual effect on the phenotype in question), when combined with a perturbation of another gene (which causes the phenotype in question), results in a mutant phenotype opposite (relative to wild type) to that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as:\nE = a < b = wt < ab\nOR\nab < wt = b < a = E\nwhere 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value." [PMID:15833125] subset: PSI-MI_slim is_a: MI:1286 ! over-suppression created_by: orchard creation_date: 2013-06-05T21:54:08Z [Term] id: MI:1296 name: amino acid analysis def: "The presence of particular residues,for example those altered through post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies." [PMID:19072539] subset: PSI-MI_slim is_a: MI:0659 ! experimental feature detection created_by: orchard creation_date: 2013-06-06T07:49:49Z [Term] id: MI:1297 name: phosphoamino acid analysis def: "The presence of amino acid residues phosphorylated as a result of post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies." [PMID:19072539] subset: PSI-MI_slim is_a: MI:1296 ! amino acid analysis created_by: orchard creation_date: 2013-06-06T07:55:30Z [Term] id: MI:1298 name: complex type def: "A classification of the structural characteristics of a macromolecular complex." [PMID:12853463] subset: PSI-MI_slim is_a: MI:0314 ! complex created_by: orchard creation_date: 2013-06-06T08:52:34Z [Term] id: MI:1299 name: complex composition def: "A description of the molecule types of which a macromolecular complex is composed." [PMID:12853464] subset: PSI-MI_slim is_a: MI:0314 ! complex created_by: orchard creation_date: 2013-06-06T08:55:37Z [Term] id: MI:1300 name: obligate complex def: "The protein chains present in the complex are not found as independent stable structures in vivo." [PMID:12853463] subset: PSI-MI_slim is_a: MI:1298 ! complex type created_by: orchard creation_date: 2013-06-06T08:57:32Z [Term] id: MI:1301 name: non-obligate complex def: "Protein chains present in the complex may also be found as independent stable proteins in vivo." [PMID:12853463] subset: PSI-MI_slim is_a: MI:1298 ! complex type created_by: orchard creation_date: 2013-06-06T09:02:52Z [Term] id: MI:1302 name: stable complex def: "A stable set (2 or more) of interacting molecules which can be co-purified and have been shown to exist as a functional unit in vivo." [PMID:12853464] subset: PSI-MI_slim is_a: MI:1298 ! complex type created_by: orchard creation_date: 2013-06-06T09:05:59Z [Term] id: MI:1303 name: transient complex def: "A macromolecular complex of which the participants associate and dissociate in vivo. Weak transient complexes feature a dynamic oligomeric equilibrium in solution where the interaction is broken and formed continuously. Strong transient associations that require a molecular trigger to shift the oligomeric equilibrium." [PMID:12853463] subset: PSI-MI_slim is_a: MI:1298 ! complex type created_by: orchard creation_date: 2013-06-06T09:09:01Z [Term] id: MI:1304 name: molecule set def: "A group of molecules linked by a high degree of similarity of sequence and/or function and not easily separated by participant identification methods." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0313 ! interactor type created_by: orchard creation_date: 2013-06-06T09:20:00Z [Term] id: MI:1305 name: candidate set def: "A group of interactors hypothesized to perform a specified function. Example: Two splice variants of Raptor mRNA encode closely related proteins. One (member) has been shown to participate in formation of active mTORC complex; the other (candidate) is thought to do so." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1304 ! molecule set created_by: orchard creation_date: 2013-06-06T10:09:09Z [Term] id: MI:1306 name: open set def: "A group of interactors that can be counted in principle but not in practice, such as mRNA or long-chain fatty acid. Examples - ceruloplasmin mRNA, palmitic acid." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1304 ! molecule set created_by: orchard creation_date: 2013-06-06T10:19:10Z [Term] id: MI:1307 name: defined set def: "Two or more interactors, grouped to denote interchangeable function. Thus the addition of a single nucleotide residue during RNA transcription could be annotated with the definedSet NTP (members ATP, CTP, GTP, and UTP)." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1304 ! molecule set created_by: orchard creation_date: 2013-06-06T10:22:53Z [Term] id: MI:1308 name: resulting sequence def: "Used to specify the identity of the residue (or residues) introduced by mutation or variant (of child terms). The attribute would be used concurrently with the description\nprovided in the feature name." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0668 ! feature attribute name created_by: orchard creation_date: 2013-06-06T10:26:19Z [Term] id: MI:1309 name: de-ADP-ribosylation assay def: "Hydrolytic reactions that release ADP-ribose." [PMID:23474712, PMID:23474714] subset: PSI-MI_slim synonym: "mono-ADP-ribosylhydrolase" EXACT [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2013-06-06T10:31:58Z [Term] id: MI:1310 name: de-ADP-ribosylation reaction def: "Measure of hydrolytic reactions that release ADP-ribose." [PMID:23474712, PMID:23474714] subset: PSI-MI_slim synonym: "mono-ADP-ribosylhydrolase reaction" RELATED [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2013-06-06T10:34:18Z [Term] id: MI:1311 name: differential scanning calorimetry def: "Differential scanning calorimetry (DSC) is a thermoanalytical technique in which the difference in the amount of heat required to increase the temperature of a sample and reference in solution is measured as a function of temperature. By measuring the temperature dependence of this partial heat capacity, a basic thermodynamic property, DSC gives immediate access to the thermodynamic mechanism that governs a conformational equilibrium, for example between a protein complex and its individual participants." [PMID:10398392] subset: PSI-MI_slim synonym: "dsc" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical created_by: orchard creation_date: 2013-06-06T10:39:30Z [Term] id: MI:1312 name: aut-page def: "Method allowing the detection of interactions between two molecules by their very close proximity or the overlap of their relative bands in a SDS gel containing urea as an additional denaturing agent." [PMID:12875839] subset: PSI-MI_slim synonym: "acetic acid/urea/triton PAGE" RELATED [] is_a: MI:0807 ! comigration in gel electrophoresis created_by: orchard creation_date: 2013-06-06T10:43:24Z [Term] id: MI:1313 name: proximity labelling technology def: "Methods depend on a modification that only takes place with the close proximity of two molecules - a protein fused to the bait can then modify any neighbouring prey proteins, for example. The resulting tag can be used for isolation and/or identification." [PMID:22412018] subset: PSI-MI_slim is_a: MI:2198 ! labelling assay created_by: orchard creation_date: 2013-06-06T11:20:43Z [Term] id: MI:1314 name: proximity-dependent biotin identification def: "A promiscuous biotin protein ligase is fused to the bait protein, neighbouring prey are then biotinylated. The biotin tag may be used for isolation and/or identification." [PMID:22412018] subset: PSI-MI_slim synonym: "BioID" RELATED [] is_a: MI:1313 ! proximity labelling technology created_by: orchard creation_date: 2013-06-06T11:23:53Z [Term] id: MI:1315 name: complex recommended name def: "The most accepted name in the literature for this complex." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1041 ! synonym created_by: orchard creation_date: 2013-10-14T15:00:37Z [Term] id: MI:1316 name: complex systematic name def: "A name for a complex built of the component parts of that complex." [] subset: PSI-MI_slim is_a: MI:1041 ! synonym created_by: orchard creation_date: 2013-10-14T15:04:57Z [Term] id: MI:1317 name: eukaryotic linear motif resource def: "The ELM resource provides a database of curated short linear motif classes and instances, as well as a sequence analysis tool to detect putative short linear motif instances in query sequences. http://elm.eu.org/" [PMID:22110040] synonym: "elm" EXACT PSI-MI-short [] xref: id-validation-regexp: "[A-Za-z_0-9]+$" xref: search-url: "http://elm.eu.org/elms/elmPages/${ac}.html" is_a: MI:0447 ! feature database created_by: orchard creation_date: 2013-10-22T09:49:10Z [Term] id: MI:1318 name: sulfate donor def: "Any molecule that is able to transfer a sulphate group to another chemical species." [PMID:14755292] subset: PSI-MI_slim synonym: "sulphate donor" RELATED [] is_a: MI:0918 ! donor created_by: orchard creation_date: 2014-01-08T07:51:29Z [Term] id: MI:1319 name: sulfate acceptor def: "Molecule to which a sulphate group may be transferred from a sulphate donor." [PMID:14755292] subset: PSI-MI_slim synonym: "sulphate acceptor" RELATED [] is_a: MI:0919 ! acceptor created_by: orchard creation_date: 2014-01-08T07:52:46Z [Term] id: MI:1320 name: membrane yeast two hybrid def: "Traditional yeast two hybrid assays are not suitable for the analysis of membrane proteins, as they require the interactions to occur in the nucleus. Methods have been specifically developed to assay for interactions of membrane proteins with both cytosolic or membrane-bound partners." [PMID:2261051] subset: PSI-MI_slim synonym: "MYTH" EXACT [] is_a: MI:0232 ! transcriptional complementation assay created_by: orchard creation_date: 2014-01-08T10:14:46Z [Term] id: MI:1321 name: ire1 reconstruction def: "Upon interaction of N-terminal generated Ire1p-fusions, the Ire1p kinase domains oligomerize, transphosphorylate and activate their C-terminal RNAseL domains, which specifically splice the mRNA of a transcriptional activator, Hac1. The expression of the mature form of Hac1p leads to the interaction-specific expression of a reporter. Specifically designed to identify interactors of proteins found in the endoplasmic reticulum." [PMID:22665516] subset: PSI-MI_slim synonym: "endoplasmic reticulum membrane yeast-two hybrid" RELATED [] synonym: "ER-MYTH" RELATED [] is_a: MI:1320 ! membrane yeast two hybrid created_by: orchard creation_date: 2014-01-08T10:17:38Z [Term] id: MI:1322 name: atto 465 def: "Fluorescent tag - maleimide couples to thiols." [PMID:14755292] subset: PSI-MI_slim synonym: "atto 465 maleimide" EXACT [] synonym: "atto465" EXACT [] is_a: MI:1092 ! atto label created_by: orchard creation_date: 2014-01-08T10:27:34Z [Term] id: MI:1323 name: tag visualisation by alkaline phosphatase activity def: "The protein is expressed as a hybrid protein fused to a tag containing an alkaline phosphatase activity. Subsequent observation or measurement of alkaline phosphatase activity is used to identify the presence of the molecule in an interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "tag alk phosphatase activity" EXACT PSI-MI-short [] is_a: MI:0980 ! tag visualisation by enzyme assay created_by: orchard creation_date: 2014-01-08T11:00:36Z [Term] id: MI:1324 name: conditioned medium def: "Molecule present in media harvested from cultured cells." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0342 ! sample process created_by: orchard creation_date: 2014-01-08T11:07:44Z [Term] id: MI:1325 name: sulfurtransferase assay def: "Measures the rate of a sulphate molecule transfer between two molecules." [PMID:14755292] subset: PSI-MI_slim synonym: "sulfertransferase" EXACT PSI-MI-short [] synonym: "sulfurtransfer assay" RELATED [] synonym: "sulphurtransferase assay" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2014-01-08T11:13:39Z [Term] id: MI:1326 name: CLONE OF phosphotransfer reaction def: "Reaction where a phosphate is transferred between two proteins of a phosphorelay system. " [PMID:14755292, PMID:16712436] subset: PSI-MI_slim synonym: "phosphotransfer" EXACT PSI-MI-short [] is_obsolete: true created_by: orchard creation_date: 2014-01-08T11:15:51Z [Term] id: MI:1327 name: sulfurtransfer reaction def: "Reaction where a sulfate group is transferred between two proteins" [GO:GO\:0016783, PMID:14755292] subset: PSI-MI_slim synonym: "sulfurtransfer" EXACT PSI-MI-short [] synonym: "sulphurtransfer reaction" EXACT [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2014-01-08T11:16:12Z [Term] id: MI:1328 name: coumarin label def: "A class of labels derived from the benzopyrone coumarin." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0857 ! fluorescent dye label created_by: orchard creation_date: 2014-01-08T11:25:00Z [Term] id: MI:1329 name: cpm def: "The thiol-reactive coumarin, CPM is very weakly fluorescent until reacted with thiols producing a conjugate with excitation/emission maxima of ~384/470 nm." [PMID:14755292] synonym: "7-diethylamino-3-(4' maleimidylphenyl)-4-methylcoumarin" EXACT [] is_a: MI:1328 ! coumarin label created_by: orchard creation_date: 2014-01-08T11:36:48Z [Term] id: MI:1330 name: dnp def: "Fluorescent dye. Also acts as an uncoupler of oxidative phosphorylation in the mitochondria." [PMID:14755292] subset: PSI-MI_slim synonym: "2, 4-DNP" EXACT [] synonym: "2,4-Dinitrophenol" EXACT [] synonym: "dinitrophenol" EXACT [] is_a: MI:0857 ! fluorescent dye label created_by: orchard creation_date: 2014-01-08T12:01:24Z [Term] id: MI:1331 name: evidence ontology def: "The Evidence Ontology (ECO) describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means." [PMID:14755292] subset: PSI-MI_slim synonym: "ECO" RELATED [] xref: id-validation-regexp: "ECO:\\d{7}$" xref: search-url: "http://www.ebi.ac.uk/ols/ontologies/ECO/terms?obo_id=${ac}" is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2014-01-08T12:48:33Z [Term] id: MI:1332 name: bhf-ucl def: "The Cardiovascular Gene Annotation Initiative represents a collaboration between University College London and the European Bioinformatics Institute (EBI), funded by the British Heart Foundation. This annotation group is a member of the IMEx Consortium." [PMID:21419760] subset: PSI-MI_slim synonym: "Cardiovascular Gene Annotation Initiative" RELATED [] is_a: MI:0461 ! interaction database is_a: MI:0973 ! imex source created_by: orchard creation_date: 2014-01-08T12:56:27Z [Term] id: MI:1333 name: rogid def: "SEGUID's are SHA-1 keys written in canonical base64 form with trailing = characters removed. ROG identifiers concatenate a SEGUID with a numerical taxonomy identifier. Therefore, the allowable characters in a SEGUID or ROG identifier are (in ascending ASCII or Unicode value):\n+/0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz\nLists of SEGUID or ROG identifiers were sorted in ascending ASCII-based lexicographical order." [PMID:18823568] subset: PSI-MI_slim is_a: MI:1212 ! checksum created_by: orchard creation_date: 2014-01-09T11:17:18Z [Term] id: MI:1334 name: rigid def: "A global unique identifier to identify interactions that are identical. A RIG identifier (RIGID) is constructed by concatenating ROGID MI:1335 (after sorting them in ascending lexicographical order ), applying the SHA-1 algorithm to the resulting string, converting the digest to its base64 representation and removing all trailing \"=\" characters used for padding." [PMID:18823568] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:1212 ! checksum created_by: orchard creation_date: 2014-01-09T11:17:32Z [Term] id: MI:1335 name: hpidb def: "Host-pathogen database. HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource. Manual curation is performed via the IntAct (ww.ebi.ac.uk/intact) curation interface.\nhttp://www.agbase.msstate.edu/hpi/main.html" [PMID:20946599] subset: PSI-MI_slim synonym: "Host Pathogen Interaction database" EXACT [] is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2014-03-03T11:43:31Z [Term] id: MI:1336 name: experiment database def: "Databases that contain information used to add additional information to experiments (meta-data)." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "experiment xref" EXACT PSI-MI-short [] is_a: MI:0444 ! database citation created_by: orchard creation_date: 2014-01-20T11:56:03Z [Term] id: MI:1337 name: efo def: "The Experimental Factor Ontology provides a systematic description of many experimental variables, combining parts of several biological ontologies to additional new terms." [pmid:20200009] subset: PSI-MI_slim synonym: "Experimental facto ontology" EXACT [] xref: id-validation-regexp: "\\d{7}$" xref: search-url: "http://www.ebi.ac.uk/ols/ontologies/efo/terms?obo_id=${ac}" is_a: MI:1336 ! experiment database created_by: orchard creation_date: 2014-01-20T11:58:47Z [Term] id: MI:1338 name: eef tag def: "Glu-Glu-Phe epitope tag, allowing its detection with rat monoclonal antibody YL1/2" [PMID:6204858] subset: PSI-MI_slim synonym: "Glu-Glu-Phe epitope tag" RELATED [] is_a: MI:0507 ! tag created_by: orchard creation_date: 2014-01-20T12:13:30Z [Term] id: MI:1339 name: supercharged green fluorescent protein def: "Mutated green fluorescent protein with altered net charge and thus altered intermolecular properties, such as resistence to aggregation." [PMID:17665911] subset: PSI-MI_slim synonym: "stGFP" RELATED [] is_a: MI:0367 ! green fluorescent protein tag created_by: orchard creation_date: 2014-01-20T13:13:03Z [Term] id: MI:1340 name: human orfeome collection def: "A central resource of single-colony, fully-sequenced cloned human ORFs which can be readily transferred to Gateway compatible destination vectors for various functional proteomics studies. This set of ORFs ranges in size from 75 to more than 10,000 base pairs, and contains over 1,000 ORFs from genes with multiple splice variants." [PMID:14755292] subset: PSI-MI_slim xref: search-url: "http://horfdb.dfci.harvard.edu/" is_a: MI:1096 ! protein sequence databases created_by: orchard creation_date: 2014-04-08T16:15:19Z [Term] id: MI:1341 name: set member def: "Indicates that this protein is a member of a set of proteins with similar sequence and/or function." [PMID:14755292, XX:] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type created_by: orchard creation_date: 2014-04-25T09:19:21Z [Term] id: MI:1342 name: qcmd def: "The quartz crystal microbalance is a physical technique that detects changes in the resonance frequency of an electrically driven quartz crystal with changes in mass. It provides qualitative and quantitative information about biomolecular interactions by translating changes in mass at the probe-immobilized surface of the crystal sensor into measurable changes in the resonant frequency of the quartz crystal. QCM-D enables real-time, label free measurements of molecular adsorption and/or interactions on various surfaces and is able to monitor conformational changes upon interactions." [PMID:19137101, PMID:22158962, PMID:23504432] subset: PSI-MI_slim synonym: "QCM-D" EXACT [] synonym: "Quartz Crystal Microbalance with Dissipation monitoring" EXACT [] is_a: MI:0968 ! biosensor created_by: orchard creation_date: 2014-07-17T08:26:51Z [Term] id: MI:1343 name: enzyme regulator def: "Regulatory subunits of enzyme complexes can determine the activity level or specificity of catalytic subunits." [PMID:14755292] subset: PSI-MI_slim synonym: "enzyme complex regulatory subunit" BROAD [] is_a: MI:2274 ! regulator created_by: orchard creation_date: 2014-07-17T08:43:17Z [Term] id: MI:1344 name: erythrosin iodoacetamide label def: "Fluoresceine-derived label." [PMID:14755292] synonym: "ErIA" EXACT [] synonym: "erythrosin-5-iodoacetamide" EXACT [] is_a: MI:0939 ! fluorescein label created_by: orchard creation_date: 2014-07-17T08:47:44Z [Term] id: MI:1345 name: rho tag def: "A 9-amino acid peptide representing C terminus of bovine rhodopsin widely used as an epitope tag. A number of anti-rhodopsin antibodies recognize this epitope." [PMID:12110672, PMID:24943310] subset: PSI-MI_slim synonym: "1D4 tag" EXACT PSI-MI-alternate [] synonym: "rho1D4 tag" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag created_by: orchard creation_date: 2014-09-19T14:24:43Z [Term] id: MI:1346 name: bmrb def: "Database for NMR spectroscopy information on biomolecules hosted at the University of Wisconsin, Madison, US." [PMID:18288446] subset: PSI-MI_slim synonym: "Biological Magnetic Resonance Data Bank" RELATED [] synonym: "BioMagResBank" RELATED [] is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2014-09-19T14:42:33Z [Term] id: MI:1347 name: protein ontology def: "PRO provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities, including specific modified forms, orthologous isoforms, and protein complexes." [PMID:24270789] subset: PSI-MI_slim synonym: "PRO" RELATED [] xref: id-validation-regexp: "[0-9]{9}|[A-Z][0-9][A-Z0-9]{3}[0-9]|[A-Z][0-9][A-Z0-9]{3}[0-9]-[1-9]+" xref: search-url: "http://pir.georgetown.edu/cgi-bin/pro/entry_pro?id=${ac}" is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2014-09-26T14:06:25Z [Term] id: MI:1348 name: chembl target def: "ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets." [] subset: PSI-MI_slim xref: regexp: "CHEMBL:[0-9]+" xref: search-url: "http://www.ebi.ac.uk/chembldb/index.php/target/inspect/${ac}" is_a: MI:0683 ! sequence database relationship: part_of MI:1349 ! chembl created_by: orchard creation_date: 2014-10-16T10:10:03Z [Term] id: MI:1349 name: chembl def: "ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets." [PMID:24214965] subset: PSI-MI_slim is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2014-10-16T10:16:54Z [Term] id: MI:1350 name: orphanet def: "Orphanet is a reference portal for information on rare diseases and orphan drugs. Its aim is to help improve the diagnosis, care and treatment of patients with rare diseases." [PMID:19058507] subset: PSI-MI_slim xref: id-validation-regexp: "^\\d+$" xref: search-url: "http://www.ebi.ac.uk/ols/ontologies/ordo/terms?obo_id=${ac}" is_a: MI:1336 ! experiment database created_by: orchard creation_date: 2014-10-16T10:27:01Z [Term] id: MI:1351 name: inferred-from def: "Refers to the original experimentally verified object from which a modelled curated complex has been derived." [PMID:25313161] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type created_by: orchard creation_date: 2014-10-16T10:39:21Z [Term] id: MI:1352 name: uracil interference assay def: "In uracil interference assays, the DNA will be amplified by PCR in the presence of a mixture of TTP and dUTP to randomly replace thymine by deoxyuracil residues before the binding assay. If T nucleotides involved in protein-DNA interactions are replaced by deoxyuracil, protein binding is prevented. After isolating the protein-DNA complex, DNA is cleaved with uracil-N-glycosylase, which specifically targets uracil bases, and the products are electrophoresed on a denaturing polyacrylamide gel. As a result, DNA in which a thymine involved in binding is replaced by uracil will be depleted. Hence, although the pattern looks like a footprint, the blank region means \"contact points\"." [PMID:18265086] subset: PSI-MI_slim is_a: MI:0605 ! enzymatic footprinting created_by: orchard creation_date: 2015-01-28T10:12:25Z [Term] id: MI:1353 name: au5 tag def: "Epitope tag engineered onto the N- or C- terminus of a protein of interest so that the tagged protein can be analyzed and visualized by immunochemical methods. The recognized AU5 epitope represents the amino acid sequence TDFYLK." [PMID:9765280] subset: PSI-MI_slim is_a: MI:0507 ! tag created_by: orchard creation_date: 2015-01-28T10:23:06Z [Term] id: MI:1354 name: lipase assay def: "Cleavage (hydrolysis) of a lipid molecule." [PMID:14760721, XX:] subset: PSI-MI_slim is_a: MI:0990 ! cleavage assay created_by: orchard creation_date: 2015-02-03T13:18:55Z [Term] id: MI:1355 name: lipid cleavage def: "Reaction monitoring the cleavage (hydrolysis) or a lipid molecule." [PMID:14760721] subset: PSI-MI_slim is_a: MI:0194 ! cleavage reaction created_by: orchard creation_date: 2015-02-03T13:25:21Z [Term] id: MI:1356 name: validated two hybrid def: "The protein pairs, often initially identified by a separate 2-hybrid screening methodology, are subjected to a rigorous re-analysis which may include independent re-screening of the entire search space, retesting the assay in different strain backgrounds, and multiple retesting of identified protein pairs reversing bait-prey orientations. Orthogonal data from other experimental and bioinformatic approaches may also be used to support the identification of the final high-confidence protein pairs but the primary means of selection must be experimentally based. This method would be expected to identify protein pairs with a higher degree of confidence than any single protein complementation technique." [PMID:25416956] subset: PSI-MI_slim is_a: MI:0018 ! two hybrid created_by: orchard creation_date: 2015-02-03T13:36:20Z [Term] id: MI:1357 name: RNAcentral def: "Provides unified access to the ncRNA sequence data supplied by the expert databases." [PMID:25352543] subset: PSI-MI_slim xref: id-validation-regexp: "/URS[0-9A-F]{10}/i" xref: search-url: "http://rnacentral.org/rna/${ac}" is_a: MI:0683 ! sequence database created_by: orchard creation_date: 2015-02-03T13:37:23Z [Term] id: MI:2002 name: drugbank def: "DrugBank Accession number consisting of the 4 letter prefix and a 5 number suffix. Each Accession number is unique to the drug's generic name. The 4 letter suffix (APRD, EXPT, BIOD, NUTR) indicates the type of drug (APRD=approved small molecule drug, EXPT=experimental drug, BIOD=biotech drug, NUTR=nutraceutical or natural product). Biotech drugs consist of FDA approved peptide, protein or nucleic acid drugs, approved small molecule drugs are FDA approved non-biotech drugs, nutraceuticals are natural products (amino acids, vitamins, other metabolites) and experimental drugs include drugs under trial, pre-clinical drugs, unapproved drugs, well known inhibitors and possible toxins." [PMID:14755292] subset: Drugable is_a: MI:2054 ! bioactive entity reference [Term] id: MI:2003 name: commercial name def: "Standard name of drug or any reagent as provided by its manufacturer." [PMID:14755292] subset: Drugable synonym: "generic name" EXACT PSI-MI-alternate [] is_a: MI:1041 ! synonym [Term] id: MI:2004 name: drug brand name def: "Alternate names of the drug, brand names from different manufacturers." [PMID:14755292] subset: Drugable is_a: MI:1041 ! synonym [Term] id: MI:2005 name: drug mixture brand name def: "Brand names and composition of mixtures that include the drug described in this DrugCard file." [PMID:14755292] subset: Drugable synonym: "mix brand name" EXACT PSI-MI-short [] is_a: MI:1041 ! synonym [Term] id: MI:2006 name: biotech product preparation def: "Description of the drug (for biotech drugs) describing its composition and/or preparation." [PMID:14755292] subset: Drugable synonym: "biotech prep" EXACT PSI-MI-short [] is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2007 name: iupac name def: "IUPAC or standard chemical name for a drug, or a chemical." [PMID:14755292] subset: Drugable is_a: MI:1041 ! synonym [Term] id: MI:2008 name: chemical formula def: "Chemical formula describing atomic or elemental composition" [PMID:14755292] subset: Drugable is_a: MI:2086 ! physicochemical attribute name [Term] id: MI:2009 name: chemical structure def: "Image of the drug structure (if small molecule) or its sequence (if biotech drug)" [PMID:14755292] subset: Drugable is_a: MI:2086 ! physicochemical attribute name [Term] id: MI:2010 name: standard inchi def: "IUPAC International Chemical Identifier (InChI) - a machine-readable character string describing a chemical structure, developed by IUPAC and the InChI Trust as a standard to allow interoperability and linking between chemical resources. The standard InChI differs from the non-standard InChI in that it is generated with a fixed set of parameters, ensuring consistency between different resources. The current version of the standard InChI software is 1.03." [PMID:14755292] subset: PSI-MI_slim synonym: "inchi id" RELATED [] synonym: "standard inchi" EXACT PSI-MI-short [] is_a: MI:1212 ! checksum is_a: MI:2091 ! structure representation attribute name [Term] id: MI:2011 name: cas registry number def: "Chemical Abstract Service identification number" [PMID:14755292] subset: Drugable is_a: MI:2054 ! bioactive entity reference [Term] id: MI:2012 name: kegg compound def: "Kyoto Encyclopedia of Genes and Genomes compound identification number (if molecule is in KEGG)" [PMID:14755292] subset: Drugable synonym: "KEGG Compound ID" EXACT PSI-MI-alternate [] is_a: MI:0470 ! kegg [Term] id: MI:2013 name: pubchem def: "NCBI's PubChem database identification number (if molecule is in PubChem).\nOBSOLETE as redudant with MI:0730" [PMID:14755292] subset: Drugable synonym: "PubChem ID" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:2015 name: pharmgkb def: "Pharmacogenomics Knowledge Base identification number (if molecule is in PharmGKB)" [PMID:14755292] subset: Drugable is_a: MI:2054 ! bioactive entity reference [Term] id: MI:2016 name: bind smid def: "BIND database Small Molecule Identification number (if molecule is in BIND)" [PMID:14755292] comment: May not be publicly available any more since now owned by Thompson Scientific. subset: Drugable is_a: MI:2054 ! bioactive entity reference [Term] id: MI:2017 name: heterogen def: "The HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for\nwhich coordinates are supplied. Groups are considered HET if they are: \n- not one of the standard amino acids, and \n- not one of the nucleic acids (C, G, A, T, U, and I), and \n- not one of the modified versions of nucleic acids (+C, +G, +A,\n+T, +U, and +I), and \n- not an unknown amino acid or nucleic acid where UNK is used to\nindicate the unknown residue name. \nHet records also describe heterogens for which the chemical identity is unknown, in which case the group is assigned the hetID UNK." [PMID:14755292] subset: Drugable synonym: "het" EXACT PSI-MI-short [] is_a: MI:0460 ! rcsb pdb is_a: MI:0472 ! pdbe is_a: MI:0806 ! pdbj [Term] id: MI:2020 name: canadian drug identification number def: "Drug Identification Number (Canadian Drug ID system)" [PMID:14755292] subset: Drugable synonym: "din" EXACT PSI-MI-short [] is_a: MI:2054 ! bioactive entity reference [Term] id: MI:2021 name: rxlist link def: "Hyperlink to RxList entry for the given drug (if it exists)" [PMID:14755292] subset: Drugable is_a: MI:2054 ! bioactive entity reference [Term] id: MI:2023 name: material safety data sheet def: "Material Safety Data Sheet (if it exists). A Material Safety Data Sheet (MSDS) is designed to provide both workers and emergency personnel with the proper procedures for handling or working with a particular substance. MSDS's include information such as physical data (melting point, boiling point, flash point etc.), toxicity, health effects, first aid, reactivity, storage, disposal, protective equipment, andspill/leak procedures. These are of particular use if a spill or other accident occurs." [PMID:14755292] subset: Drugable synonym: "msds" EXACT PSI-MI-short [] synonym: "MSDS Material Safety Sheet" EXACT PSI-MI-alternate [] is_a: MI:2086 ! physicochemical attribute name [Term] id: MI:2024 name: patent number def: "number of the patent describing a drug's synthesis or use." [PMID:14755292] subset: Drugable is_a: MI:0353 ! cross-reference type [Term] id: MI:2025 name: molecular weight def: "Molecular weight in g/mol, determined from molecular formula or sequence." [PMID:14755292] subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2026 name: melting point def: "The melting point of a solid is the temperature range at which it changes state from solid to liquid." [PMID:14755292] subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2027 name: water solubility def: "Water solubility in mg/mL or g/L" [PMID:14755292] subset: Drugable synonym: "logSw" EXACT PSI-MI-alternate [] is_a: MI:2160 ! logs [Term] id: MI:2029 name: logp def: "Water/octanol partition coefficient of a small molecule." [PMID:14755292] subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2030 name: isoelectric point def: "The isoelectric point (pI) is the pH at which a particular molecule or surface carries no net electrical charge. For an amino acid with only one amine and one carboxyl group, the pI can be calculated from the pKas of this molecule." [PMID:14755292] subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2033 name: hydrophobicity def: "Physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water. Gravy score." [PMID:14755292] subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2036 name: boiling point def: "The boiling point of a liquid is the temperature at which the vapor pressure of the liquid equals the environmental pressure surrounding the liquid. A liquid in a vacuum environment has a lower boiling point than when the liquid is at atmospheric pressure. A liquid in a high pressure environment has a higher boiling point than when the liquid is at atmospheric pressure. In other words, the boiling point of liquids varies with and depends upon the surrounding environmental pressure." [PMID:14755292] subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2039 name: smiles string def: "SMILES string corresponding to drug structure" [PMID:14755292] subset: Drugable is_a: MI:1212 ! checksum is_a: MI:2091 ! structure representation attribute name [Term] id: MI:2040 name: drug type def: "Type of drug (approved, experimental, biotech, nutraceutical)" [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2041 name: drug category def: "Therapeutic category or general category of drug (anti-convulsant, antibacterial, etc.)." [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2042 name: disease indication def: "Description or common names of diseases that the drug is used to treat." [PMID:14755292] comment: Source of further terms could be MeSH term or SNOWMAN. subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2043 name: pharmacology def: "Text description of how the drug works at a clinical or physiological level." [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2044 name: mechanism of action def: "Description of how the drug works or what it binds to at a molecular level." [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2045 name: drug absorption def: "Determination of how quickly and how much of a drug reaches its intended target (site) of action." [PMID:14755292] subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2046 name: lethal dose 50 def: "The LD50 is the dose that kills half (50%) of the animals tested" [PMID:14755292] subset: Drugable synonym: "ld50" EXACT PSI-MI-alternate [] synonym: "lethal dose 50 %" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:2047 name: percentage of plasma protein binding def: "Percentage of the drug that is bound in plasma proteins" [PMID:14755292] subset: Drugable synonym: "plasma prot binding" EXACT PSI-MI-short [] synonym: "protein binding %" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:2048 name: drug biotransformation def: "The chemical conversion of drugs to other compounds in the body, excluding degradation due to any inherent chemical instability of drugs in biological media." [PMID:14755292] subset: Drugable synonym: "drug metabolism" EXACT PSI-MI-short [] is_a: MI:2115 ! pharmacokinetics attribute name [Term] id: MI:2049 name: elimination half life def: "Rate The time it takes for the body to eliminate or breakdown half of a dose of a pharmacologic agent, in practice the time taken for plasma concentration to reduce by 50%." [PMID:14755292] subset: Drugable synonym: "distribution halflife" EXACT PSI-MI-alternate [] synonym: "elimin half life" EXACT PSI-MI-short [] synonym: "t1/2" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:2050 name: dosage form def: "How the drug is dispensed (tablets, capsules, solutions), packing material." [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2051 name: patient information def: "Information on the disease indications and treatment regime for the drug. May also include contra-indications." [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2053 name: contraindications def: "Cautions or conditions indicating why or when the drug should not be taken or prescribed." [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2054 name: bioactive entity reference def: "General on-line reference to other details about a drug or other bioactive entity." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "bioactive entity ref" EXACT PSI-MI-short [] is_a: MI:0473 ! participant database [Term] id: MI:2055 name: chemical stability def: "chemical stability occurs when a substance is in a (dynamic) chemical equilibrium with its environment. In this well-defined state, the substance is expected to persist indefinitely (assuming that the environment does not change). A substance which is not chemically stable (yet exists) is metastable or kinetically persistent." [PMID:14755292] subset: Drugable synonym: "thermodynamic stability" EXACT PSI-MI-alternate [] is_a: MI:2086 ! physicochemical attribute name [Term] id: MI:2064 name: solubility def: "Potential ability of a substance to dissolve in a liquid." [PMID:14755292] subset: Drugable synonym: "dt theoretical pi" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:2084 name: organisms affected def: "Names of organisms which are affected, positively or negatively, by the drug." [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2086 name: physicochemical attribute name def: "Chemical and physical properties of a molecule." [PMID:14755292] subset: Drugable synonym: "physicochemical att" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:2089 name: bioactive entity attribute name def: "Properties of a chemical tested or used as a drug, herbicide, insecticide etc." [PMID:14755292] subset: Drugable synonym: "bioactive entity att" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:2091 name: structure representation attribute name def: "Human artefact to describe and report the structure of a molecule." [PMID:14755292] subset: Drugable synonym: "struc representation" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:2097 name: anti-convulsant def: "Therapeutic category or general category of drug -anti-convulsant" [PMID:14755292] subset: Drugable is_a: MI:2041 ! drug category [Term] id: MI:2098 name: anti-bacterial def: "Therapeutic category or general category of drug -anti-bacterial" [PMID:14755292] subset: Drugable is_a: MI:2041 ! drug category [Term] id: MI:2099 name: fda approved drug def: "A drug licensed for sale in the USA by the FDA." [PMID:14755292] subset: Drugable is_a: MI:2040 ! drug type [Term] id: MI:2100 name: experimental drug def: "A drug which has yet to be formally approved for the indication which it is currently being used to treat." [PMID:14755292] subset: Drugable is_a: MI:2040 ! drug type [Term] id: MI:2101 name: biotech drug def: "A natural product, such as a protein or peptide, which is produced used biotechnology as a drug." [PMID:14755292] subset: Drugable is_a: MI:2040 ! drug type [Term] id: MI:2102 name: nutraceutical drug def: "A drug which may also be regarded as a foodstuff." [PMID:14755292] subset: Drugable is_a: MI:2040 ! drug type [Term] id: MI:2105 name: pka def: "Negative decimal logarithm of Ka, acid dissociation equilibrium constant for the dissociation of a weak acid." [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2106 name: degree of ionisation ph 7.4 def: "The degree of ionization refers to the proportion of neutral particles such as those in a gas or aqueous solution, that are ionized into charged particles. A low degree of ionization is sometimes called partially ionized, and a very high degree of ionization as fully ionized. This measurment is performed at pH 7.4" [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "ionisation ph 7.4" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:2107 name: logd def: "The LogD is the ratio of the equilibrium concentrations of all species (unionized and ionized) of a molecule in octanol to same species in the water phase at a given temperature, normally 25 C. It differs from LogP in that ionized species are considered as well as the neutral form of the molecule.pH 7.4" [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2108 name: solubility ph 7.4 def: "Solubility pH 7.4" [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable is_a: MI:2064 ! solubility [Term] id: MI:2109 name: solubility in dmso def: "Solubility in DMSO" [PMID:14755292] subset: Drugable is_a: MI:2064 ! solubility [Term] id: MI:2111 name: diffusion coefficient def: "Diffusion coefficient D is proportional to the velocity of the diffusing particles, which depends on the temperature, viscosity of the fluid and the size of the particles according to the Stokes-Einstein relation. In dilute aqueous solutions the diffusion coefficients of most ions are similar and have values that at room temperature are in the range of 0.6x10-9 to 2x10-9 m2/s. For biological molecules the diffusion coefficients normally range from 10-11 to 10-10 m2/s." [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "diffusion coeff" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:2112 name: chemical stability at pH 2 def: "Chemical stability at pH 2" [PMID:14755292] comment: Qualitative prediction of this parameter is possible. subset: Drugable synonym: "chem stab ph 2" EXACT PSI-MI-short [] is_a: MI:2055 ! chemical stability [Term] id: MI:2113 name: dissolution profile def: "The rate of dissolution is a key target for controlling the duration of a drug's effect, and as such, several dosage forms that contain the same active ingredient may be available, differing only in the rate of dissolution. If a drug is supplied in a form that is not readily dissolved, the drug may be released more gradually over time with a longer duration of action. Having a longer duration of action may improve compliance since the medication will not have to be taken as often. Additionally, slow-release dosage forms may maintain concentrations within an acceptable therapeutic range over a long period of time, as opposed to quick-release dosage forms which may result in sharper peaks and troughs in serum concentrations." [PMID:14755292] comment: The prediction of the value for this paramter is currently not possible. subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2115 name: pharmacokinetics attribute name def: "Determination of the fate of substances administered externally to a living organism i.e. the study of what the body does to a drug." [PMID:14755292] subset: Drugable is_a: MI:2086 ! physicochemical attribute name [Term] id: MI:2116 name: cell permeability def: "The permitting or activating of the passage of substances into, out of, or through cells." [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2118 name: volume of distribution def: "The Volume of Distribution is the amount of drug in the body divided by the concentration in the blood. Drugs that are highly lipid soluble have a very high volume of distribution (500 litres). Drugs which are lipid insoluble remain in the blood, and have a low Vd." [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "distribution volume" EXACT PSI-MI-alternate [] synonym: "vd" EXACT PSI-MI-alternate [] synonym: "vol of distribution" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:2120 name: tissue distribution def: "Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2121 name: transporter binding def: "Substrate of a carrier system allowing the intake of an agent into an organ or part of body." [PMID:14755292] comment: The prediction of the value for this parameter is currently not possible. subset: Drugable is_a: MI:2115 ! pharmacokinetics attribute name [Term] id: MI:2122 name: clearance def: "The ratio of excretion is or measure of the speed at which a constituent is lost from the body." [PMID:14755292] subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2123 name: renal clearance def: "The renal clearance ratio or fractional excretion is a measure of the speed at which a constituent of urine passes through the kidneys, in this context the rate at which a pharmacological agent is lost from the body via urine." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2124 name: total clearance def: "The clearance of a drug is the volume of plasma from which the drug is completely removed per unit time. The amount eliminated is proportional to the concentration of the drug in the blood." [PMID:14755292] comment: The prediction of the value for this paramter is currently not possible. subset: Drugable synonym: "cl" EXACT PSI-MI-alternate [] synonym: "clearance" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:2125 name: maximum absorbable dose def: "The Maximum Absorbable Dose (MAD) represents the amount of drug that can permeate across a barrier." [PMID:8987073] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "mad" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:2126 name: paracellular absorption def: "Water soluble compounds are absorbed in the small intestine mainly via two pathways, the transcellular and the paracellular pathways. The paracellular absorption involves movement of solutes through a restrictive aqueous channel in the tight junctions of adjoining cells by diffusion." [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "paracellular absorp" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:2127 name: tmax/cmax def: "Ratio between the time value at Cmax (maximum concentration) in a dose response curve, and the Cmax value itself." [PMID:14755292] comment: The prediction of the value for this paramter is currently not possible. subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2128 name: ABCB1 transporter substrate def: "Substrate for the representitive member of the ABC transprorter family ABCB1 (MDR1, pgy1, P08183). ABC transporters preventing uptake or facilitating clearance of toxic substances, playing an important role in drug excretion through the bile." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable synonym: "abcb1 substrate" EXACT PSI-MI-short [] synonym: "pgp(mdr1) substrate " EXACT PSI-MI-alternate [] is_a: MI:2121 ! transporter binding [Term] id: MI:2129 name: bile transporter substrate def: "Substrate of the bile acid carrier system in both the intestinal tract and the liver. System catalyses of the transfer of bile acid from one side of the membrane to the other. Bile acids are any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine." [PMID:14755292] comment: The prediction of the value for this paramater is currently not possible. subset: Drugable synonym: "bile trans substrate" EXACT PSI-MI-short [] is_a: MI:2121 ! transporter binding [Term] id: MI:2130 name: cyp-450 inhibition def: "Inhibitor of one or more of the family of cytochrome p450 enzymes, probably the most important elements of oxidative metabolism of exogenous compounds." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable synonym: "cyp-450 inhibition" EXACT PSI-MI-alternate [] synonym: "Cytochrome P450 inhibition" EXACT PSI-MI-alternate [] is_a: MI:2135 ! toxicity attribute name [Term] id: MI:2131 name: metabolite identification def: "Identification of the breakdown products of a substance, either through chemical instability or the actions of enzymes within the body" [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable synonym: "metabolite identific" EXACT PSI-MI-short [] is_a: MI:2115 ! pharmacokinetics attribute name [Term] id: MI:2132 name: gsh adducts def: "Derivative molecule which has formed from a reaction with glutathione." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:2115 ! pharmacokinetics attribute name [Term] id: MI:2133 name: neutralization by glucuronidation or sulfatation def: "Neutralization of a compound occuring via its glucuronidation or sulfatation." [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "neutraliz gluc/sulf" EXACT PSI-MI-short [] is_a: MI:2048 ! drug biotransformation [Term] id: MI:2135 name: toxicity attribute name def: "The mechanism by which a substance can harm humans or animals." [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2136 name: herg binding def: "Binds to the hERG (human Ether-a-go-go Related Gene) (Q12809) which encodes the Kv11.1 potassium ion channel responsible for the repolarizing IKr current in the cardiac action potential." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:2135 ! toxicity attribute name [Term] id: MI:2137 name: genotoxicity def: "Tendency of a bioactive entity to induce damage at the level of the gene." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:2135 ! toxicity attribute name [Term] id: MI:2138 name: mutagenicity def: "Tendency of a bioactive entity to induce genetic mutations at the nucleotide level e.g. substitution of nucleotide base-pairs and insertions and deletions of one or more nucleotides in DNA sequences." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:2135 ! toxicity attribute name [Term] id: MI:2139 name: carcinogenicity def: "Tendency of a bioactive entity to induce a cancer." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable synonym: "cancerogenicity" EXACT PSI-MI-alternate [] is_a: MI:2135 ! toxicity attribute name [Term] id: MI:2140 name: chromosome damage def: "Tendency of a bioactive entity to induce damage at the level of the chromosome e.g. induce a change in chromosome structure and number." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:2135 ! toxicity attribute name [Term] id: MI:2141 name: hepatotoxicity def: "Tendency of a bioactive entity to affect liver function." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:2135 ! toxicity attribute name [Term] id: MI:2142 name: phospholipidosis def: "Causes excess phospholipids to accumulate within cells." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:2135 ! toxicity attribute name [Term] id: MI:2145 name: solubility ph 6.5 def: "Solubility pH 6.5." [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable is_a: MI:2064 ! solubility [Term] id: MI:2146 name: solubility ph 2.0 def: "Solubility pH 2.0" [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "solubility ph2.0" EXACT PSI-MI-alternate [] is_a: MI:2064 ! solubility [Term] id: MI:2147 name: chemical stability at pH 7.4 def: "Chemical stabilityat at pH 7.4" [PMID:14755292] comment: Qualitative prediction of this parameter is possible. subset: Drugable synonym: "chem stab ph 7.4" EXACT PSI-MI-short [] is_a: MI:2055 ! chemical stability [Term] id: MI:2148 name: investigational drug def: "A drug currently under clinical development." [PMID:14755292] comment: Intact. subset: Drugable is_a: MI:2040 ! drug type [Term] id: MI:2149 name: withdrawn drug def: "A drug for which the licencing for prescriptive use has been withdrawn." [PMID:14755292] comment: Intact. subset: Drugable is_a: MI:2040 ! drug type [Term] id: MI:2150 name: illicit drug def: "A drug which has not been approved for sale, a drug taken for recreational purposes or a licensed drug sold without a prescription." [PMID:14755292] subset: Drugable is_a: MI:2040 ! drug type [Term] id: MI:2151 name: other drug interaction def: "Effect of additional drug treatments on a given drug action." [PMID:14755292] subset: Drugable synonym: "drug interaction" EXACT PSI-MI-short [] is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2152 name: food interaction def: "Effect of food ingestion on a given drug treatment." [PMID:14755292] comment: IntAct MeSH term or SNOWMAN. subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2153 name: pdr health def: "Hyperlink to PDRhealth entry for the given drug (if it exists)" [PMID:14755292] subset: Drugable synonym: "PDRhealth" EXACT PSI-MI-alternate [] is_a: MI:2054 ! bioactive entity reference [Term] id: MI:2154 name: wikipedia def: "Hyperlink to wikipedia entry for the given drug (if it exists)" [PMID:14755292] subset: Drugable is_a: MI:2054 ! bioactive entity reference [Term] id: MI:2155 name: average molecular weight def: "Molecular weight in g/mol, determined from molecular formula or sequence." [PMID:14755292] subset: Drugable synonym: "avrg mol weight" EXACT PSI-MI-short [] is_a: MI:2025 ! molecular weight [Term] id: MI:2156 name: monoisotopic molecular weight def: "Molecular weight in g/mol, determined from molecular formula or sequence." [PMID:14755292] subset: Drugable synonym: "monoisotopic mol wgt" EXACT PSI-MI-short [] is_a: MI:2025 ! molecular weight [Term] id: MI:2157 name: experimental water solubility def: "Water solubility in mg/mL or g/L." [PMID:14755292] subset: Drugable synonym: "exp h2o solubilty" EXACT PSI-MI-short [] synonym: "experimental h2o solubility" EXACT PSI-MI-alternate [] is_a: MI:2027 ! water solubility is_a: MI:2161 ! experimental logs [Term] id: MI:2158 name: predicted water solubility def: "Water solubility in mg/mL or g/L" [PMID:14755292] subset: Drugable synonym: "predicted h2o solub" EXACT PSI-MI-short [] synonym: "predicted h2o solubility" EXACT PSI-MI-alternate [] is_a: MI:2027 ! water solubility [Term] id: MI:2160 name: logs def: "Solubility of a molecule in a given solvant." [PMID:14755292] subset: Drugable synonym: "logS" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:2161 name: experimental logs def: "Experimental derived value for the solubility of a molecule in a given solvant." [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "experimental logS" EXACT PSI-MI-alternate [] is_a: MI:2160 ! logs [Term] id: MI:2162 name: experimental CaCO2 permeability def: "Experimentally derived value for ability of a compound to cross epithelial and endothelial cell barriers Using the CaCo2 cell line derived from a human colorectal adenocarcinoma. Used as an in vitro permeability models to predict human intestinal absorption" [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "caco2 permeability" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:2163 name: by homology def: "Reference assigned to a molecule by sequence homology with another similar sequence." [PMID:14755292] subset: Drugable is_a: MI:0353 ! cross-reference type [Term] id: MI:2164 name: mind def: "The Membrane-based Interactome Network Database (MIND) holds a network of over 25,000 putative PPI (PPPI) obtained by screening of over 3,000 unique Arabidopsis ORFs for pair-wise interactions using the yeast mating-based split-ubiquitin system (mbSUS). http://cas-biodb.cas.unt.edu/project/mind/index.php" [PMID:14755292] subset: PSI-MI_slim is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2013-02-26T12:27:35Z [Term] id: MI:2165 name: bar def: "The Arabidopsis Interactions Viewer of BAR (the Bio-Array Resource for plant biology) queries a database of 70944 predicted and 28556 confirmed Arabidopsis interacting proteins. The predicted interactions (interologs) were generated by Drs Matt Geisler and Jane Geisler-Lee at the Southern Illinois University. Their current version is Interactome 2.0. The confirmed Arabidopsis interacting proteins come from BIND, the Biomolecular Interaction Network Database, from high-density Arabidopsis protein microarrays, from Braun et al.'s Arabidopsis Interactome 2011 , from Wolf Frommer's Membrane protein INteractome Database MIND, from Etsuko Moryiama's Arabidopsis G-signaling Interactome Database, and over 1190 other literature sources. The interactions in BIND were identified using several different methods, such as yeast two hybrid screens, but also via traditional biochemical methods. http://bar.utoronto.ca/interactions/cgi-bin/arabidopsis_interactions_viewer.cgi\" [PMID:15960624]" [PMID:15960624] subset: PSI-MI_slim synonym: "bar-arabidopsis interactions viewer" EXACT [] is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2013-02-26T12:49:13Z [Term] id: MI:2166 name: ai def: "The Arabidopsis Interactome network map is a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing ~6,200 highly reliable interactions between ~2,700 proteins.\n http://interactome.dfci.harvard.edu/A_thaliana/index.php" [PMID:21798944] subset: PSI-MI_slim synonym: "AI" EXACT [] is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2013-02-26T12:54:32Z [Term] id: MI:2167 name: kinetic exclusion assay def: "In the kinetic exclusion assay one of the interaction components (bait) is immobilized to a solid phase (beads) and is used to capture the prey from a solution containing free molecules of both the prey and the bait that has reached kinetic equilibrium. This mixture of free components is only allowed to contact the immobilized bait for a very short time, so bait-prey complexes do not dissociate. The immobilized bait captures a small percentage of the prey, which is proportional to the free prey concentration, and the captured prey is detected usually via a fluorescent tag." [PMID:15674023] subset: PSI-MI_slim synonym: "kinetic exclusion" EXACT PSI-MI-short [] synonym: "kinexa" EXACT PSI-MI-alternate [] is_a: MI:0892 ! solid phase assay created_by: ppm creation_date: 2015-04-27T15:51:46Z [Term] id: MI:2168 name: conditional site labelling def: "The interaction is detected through labelling of a specific site -which can be an active site- that is only accessible once the participants are interacting. This conditional site is then marked with a chemical label for detection." [PMID:19416890] subset: PSI-MI_slim synonym: "active site labelling" RELATED [] is_a: MI:1313 ! proximity labelling technology created_by: ppm creation_date: 2015-04-29T10:19:28Z [Term] id: MI:2169 name: luminiscence technology def: "Techniques based upon the measurement of the emission of one or more photons in a bioluminescent reaction. Such reactions are typically catalyzed by two groups of enzymes: photoproteins and luciferases. Photoproteins emit light in proportion to the concentration of the protein itself, while in a luciferin-luciferase reaction, photon emission is directly proportional to the amount of luciferin." [PMID:24166364] is_a: MI:0013 ! biophysical created_by: ppm creation_date: 2015-04-29T11:50:41Z [Term] id: MI:2170 name: bimolecular luminiscence complementation def: "The bimolecular luminescence complementation (BiLC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two fragments of a bioluminescent enzyme such as luciferin or aequorin. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional bioluminescent enzyme that can be identified through microscopy or luminescence detection." [PMID:25859972] synonym: "bilc" EXACT PSI-MI-short [] synonym: "bioluminescence complementation" EXACT PSI-MI-alternate [] synonym: "bioluminescence complementation assay" EXACT PSI-MI-alternate [] synonym: "luminescence complementation assay" EXACT PSI-MI-alternate [] synonym: "luminiscence complementation" EXACT PSI-MI-alternate [] synonym: "split-luciferase complementation" RELATED [] synonym: "split-luciferase complementation assay" RELATED [] is_a: MI:2169 ! luminiscence technology created_by: ppm creation_date: 2015-04-29T12:03:27Z [Term] id: MI:2171 name: complemented donor-acceptor resonance energy transfer def: "This technology is based on quantifying the BRET between a pair of participants bearing complementation tags and a participant tagged with a bioluminescent enzyme or a fluorescent tag. The tags held by the pair of participants are complementary halves of either a fluorescent tag (N- and C- fragments of the Venus fluorescent protein, for example) or a bioluminescent enzyme (N- and C- fragments of Renilla luciferase, for example). Interaction between the pair of participants leads to reconstruction of the bioluminescent enzyme/fluorescent protein, which can then emit/accept photons that are accepted/emitted by the tag in the third participant, generating the signal used to detect the interaction. The signals emitted by the bioluminescent enzyme and the fluorescent tag have different wavelengths, so they can be distinguished." [PMID:21785426, PMID:25706338] subset: PSI-MI_slim synonym: "bret complementation" EXACT PSI-MI-alternate [] synonym: "bret complementation assay" EXACT PSI-MI-alternate [] synonym: "copa-ret" EXACT PSI-MI-short [] is_a: MI:0051 ! fluorescence technology is_a: MI:2169 ! luminiscence technology created_by: ppm creation_date: 2015-04-29T13:25:55Z [Term] id: MI:2172 name: aspgd def: "AspGD is an organized collection of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). AspGD contains information about genes and proteins of multiple Aspergillus species; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Aspergillus species.\nwww.aspergillusgenome.org/" [PMID:24194595] synonym: "Aspergillus Genome Database" EXACT PSI-MI-alternate [] synonym: "aspgd" EXACT PSI-MI-short [] synonym: "AspGD" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "ASPL[0-9]{10}" xref: search-url: "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=${ac}" is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2015-05-05T14:28:59Z [Term] id: MI:2173 name: cgd def: "Candida Genome Database is a resource for genomic sequence data and gene and protein information for Candida albicans and related species. CGD is based on the Saccharomyces Genome Database and is funded by the National Institute of Dental & Craniofacial Research at the US National Institutes of Health.\nwww.candidagenome.org/" [PMID:22064862] synonym: "Candida Genome Database" EXACT PSI-MI-alternate [] synonym: "cgd" EXACT PSI-MI-short [] synonym: "CGD" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "(CAL|CAF)[0-9]{7}" xref: search-url: "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=${ac}" is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2015-05-05T14:41:00Z [Term] id: MI:2174 name: ecoliwiki def: "Community annotation portal associated with PortEco (formerly EcoliHub, http://porteco.org/). It aims to generate community-based pages about\neverything related to non-pathogenic E. coli, its phages, plasmids, and\nmobile genetic elements.\nhttp://ecoliwiki.net/colipedia/" [PMID:22064863] synonym: "ecoliwiki" EXACT PSI-MI-short [] synonym: "EcoliWiki" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[A-Za-z]{3,4}" xref: search-url: "http://ecoliwiki.net/colipedia/${ac}" is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2015-05-05T14:55:06Z [Term] id: MI:2175 name: genedb def: "The GeneDB project is a core part of the Sanger Institute's Pathogen Genomics activities. Its primary goals are:\n-to provide reliable access to the latest sequence data and annotation/curation for the whole range of organisms sequenced by the Pathogen group.\n-to develop the website and other tools to aid the community in accessing and obtaining the maximum value from these data.\nGeneDB currently provides access to more than 40 genomes, at various stages of completion, from early access to partial genomes with automatic annotation through to complete genomes with extensive manual curation.\nwww.genedb.org" [PMID:22116062] synonym: "GeneDB" EXACT PSI-MI-alternate [] synonym: "genedb" EXACT PSI-MI-short [] xref: id-validation-regexp: "((LmjF|LinJ|LmxM)\\.[0-9]{2}\\.[0-9]{4})|(PF3D7_[0-9]{7})|(Tb[0-9]+\\.[A-Za-z0-9]+\\.[0-9]+)|(TcCLB\\.[0-9]{6}\\.[0-9]+)" xref: search-url: "www.genedb.org/gene/${ac}" is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2015-05-05T15:04:16Z [Term] id: MI:2176 name: gramene def: "Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. Gramene currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations.\nhttp://www.gramene.org" [PMID:24217918] synonym: "gramene" EXACT PSI-MI-short [] synonym: "Gramene" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "[A-Z][0-9][A-Z0-9]{3}[0-9]" xref: search-url: "http://tools.gramene.org/search?query=${ac}" is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2015-05-05T15:12:03Z [Term] id: MI:2177 name: pombase def: "PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets. \nwww.pombase.org" [PMID:22039153] synonym: "pombase" EXACT PSI-MI-short [] synonym: "PomBase" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "S\\w+(\\.)?\\w+(\\.)?" xref: search-url: "www.pombase.org/spombe/result/${ac}" is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2015-05-05T15:17:42Z [Term] id: MI:2178 name: agi_locuscode def: "The Arabidopsis Genome Initiative comprises TAIR, TIGR and MIPS." [] synonym: "agi_locuscode" EXACT PSI-MI-short [] synonym: "AGI_LocusCode" EXACT PSI-MI-alternate [] synonym: "Arabidopsis Genome Initiative" EXACT PSI-MI-alternate [] xref: id-validation-regexp: "A[Tt][MmCc0-5][Gg][0-9]{5}(\\.[0-9]{1})?" xref: search-url: "http://arabidopsis.org/servlets/TairObject?type=locus&name=${ac}" is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2015-05-05T16:12:18Z [Term] id: MI:2179 name: subset def: "Reference to the corresponding object in another database. It implies the object is part of a cross-referenced entity (usually a complex)." [PMID:14755292] subset: PSI-MI_slim synonym: "part of" EXACT PSI-MI-alternate [] synonym: "subset" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type created_by: ppm creation_date: 2015-05-11T09:59:36Z [Term] id: MI:2180 name: agbase def: "AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products. Their long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. They use the Gene Ontology for functional annotation.\nhttp://www.agbase.msstate.edu/" [PMID:21075795] subset: PSI-MI_slim synonym: "agbase" EXACT PSI-MI-short [] synonym: "AgBase" EXACT PSI-MI-alternate [] xref: search-url: "http://www.agbase.msstate.edu/cgi-bin/getEntry.pl?db_pick=[ChickGO/MaizeGO]&uid=${ac}" is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2015-05-11T10:23:14Z [Term] id: MI:2181 name: cacao def: "The Community Assessment of Community Annotation with Ontologies (CACAO) is a project to do large-scale manual community annotation of gene function using the Gene Ontology as a multi-institution student competition.\nhttp://gowiki.tamu.edu/wiki/index.php/Category:CACAO" [] subset: PSI-MI_slim synonym: "cacao" EXACT PSI-MI-short [] synonym: "CACAO" EXACT PSI-MI-alternate [] synonym: "Community Assessment of Community Annotation with Ontologies" EXACT PSI-MI-alternate [] xref: search-url: "http://gowiki.tamu.edu/wiki/index.php/${ac}" is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2015-05-11T10:51:57Z [Term] id: MI:2182 name: dflat def: "Database dedicated to annotating gene function related to human fetal development using the Gene Ontology for functional annotation.\nhttp://bcb.cs.tufts.edu/dflat/" [] subset: PSI-MI_slim synonym: "Developmental FunctionaL Annotation at Tufts" EXACT PSI-MI-alternate [] synonym: "dflat" EXACT PSI-MI-short [] synonym: "DFLAT" EXACT PSI-MI-alternate [] is_a: MI:0473 ! participant database created_by: ppm creation_date: 2015-05-11T11:01:34Z [Term] id: MI:2183 name: go_central def: "The GO Consortium coordinated an effort to maximize and optimize GO annotations for a large and representative set of key genomes, known as 'reference genomes'. The Reference Genome Annotation Project aimed to completely annotate twelve reference genomes, producing a resource that may effectively seed automatic annotation efforts of other genomes. This resource represents manual annotation from PAINT curators into the UniProt Protein2GO curation tool.\nhttp://www.geneontology.org/GO.refgenome.shtml" [PMID:19578431] subset: PSI-MI_slim synonym: "GO central" EXACT PSI-MI-alternate [] synonym: "go_central" EXACT PSI-MI-short [] synonym: "GO_central" EXACT PSI-MI-alternate [] synonym: "The Reference Genome Annotation Project" EXACT PSI-MI-alternate [] is_a: MI:0448 ! gene ontology created_by: ppm creation_date: 2015-05-11T11:10:30Z [Term] id: MI:2184 name: mtbbase def: "Collection and Refinement of Physiological Data on Mycobacterium tuberculosis in the form of GO annitations. MTBBASE data has also been rendered as pathway information in Reactome. \nhttp://www.ark.in-berlin.de/Site/MTBbase.html\nhttp://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_121237.1" [] subset: PSI-MI_slim synonym: "MTBBASE" EXACT PSI-MI-alternate [] synonym: "mtbbase" EXACT PSI-MI-short [] is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2015-05-11T11:34:15Z [Term] id: MI:2185 name: parkinsonsuk-ucl def: "The Parkinson's UK Gene Ontology Project represents a collaboration between University College London and the European Bioinformatics Institute (EBI), funded by Parkinson's UK. This annotation group is a member of the IMEx Consortium.\nhttp://www.ucl.ac.uk/functional-gene-annotation/neurological" [] subset: PSI-MI_slim synonym: "Parkinson-UCL" EXACT PSI-MI-alternate [] synonym: "Parkinsons Disease Gene Ontology Initiative" EXACT PSI-MI-alternate [] synonym: "ParkinsonsUK-UCL" EXACT PSI-MI-alternate [] synonym: "parkinsonsuk-ucl" EXACT PSI-MI-short [] is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2015-05-11T11:45:34Z [Term] id: MI:2186 name: alut def: "The Alzheimers-University of Toronto project adds functional annotation to Alzheimer's related gene products using the Gene Ontology.\nhttp://www.ims.utoronto.ca/" [] subset: PSI-MI_slim synonym: "alut" EXACT PSI-MI-short [] synonym: "Alzheimers Project at University of Toronto" EXACT PSI-MI-alternate [] synonym: "Alzheimers University of Toronto" EXACT PSI-MI-alternate [] synonym: "Alzheimers_University_of_Toronto" EXACT PSI-MI-alternate [] is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2015-05-11T13:13:02Z [Term] id: MI:2187 name: ri def: "The Roslin Institute uses the Gene Ontology to add functional annotation to different gene products.\nhttp://www.roslin.ac.uk/" [] subset: PSI-MI_slim synonym: "ri" EXACT PSI-MI-short [] synonym: "RI" EXACT PSI-MI-alternate [] synonym: "Roslin Institute" EXACT PSI-MI-alternate [] synonym: "roslin_institute" EXACT PSI-MI-alternate [] synonym: "Roslin_Institute" EXACT PSI-MI-alternate [] is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2015-05-11T13:18:36Z [Term] id: MI:2188 name: par-clip def: "Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) is a biochemical method used for identifying the binding sites of cellular RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs). The method relies on the incorporation of photoreactive ribonucleoside analogs, such as 4-thiouridine (4-SU) and 6-thioguanosine (6-SG) into nascent RNA transcripts by living cells. Irradiation of the cells by UV light of 365 nm induces efficient crosslinking of photoreactive nucleoside-labeled cellular RNAs to interacting RBPs. Immunoprecipitation of the RBP of interest is followed by isolation of the crosslinked and coimmunoprecipitated RNA. The isolated RNA is converted into a cDNA library and deep sequenced using next-generation sequencing technology.\nhttp://en.wikipedia.org/wiki/PAR-CLIP" [PMID:20371350, PMID:20644507] subset: PSI-MI_slim synonym: "PAR-CLIP" EXACT PSI-MI-alternate [] synonym: "par-clip" EXACT PSI-MI-short [] synonym: "Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation" EXACT PSI-MI-alternate [] is_a: MI:2191 ! clip created_by: ppm creation_date: 2015-05-11T15:13:05Z [Term] id: MI:2189 name: avexis def: "Low-affinity interaction detection method designed specifically to detect interactions between extracellular proteins. Recombinant soluble fragments of these proteins are produced in a (generally) mammalian expression cell line and secreted into the medium and produced in two forms: a biotinylated bait which can be captured on a streptavidin-coated solid phase suitable for screening, and a pentamerised enzyme-tagged (beta-lactamase) prey. The bait and prey proteins are presented to each other in a binary fashion to detect direct interactions between them, similar to a conventional ELISA. The pentamerisation of the proteins in the prey is achieved through a peptide sequence from the cartilage oligomeric matrix protein (COMP) and increases the local concentration of the ectodomains thereby providing significant avidity gains to enable even very transient interactions to be detected. By normalising the activities of both the bait and prey to predetermined levels prior to screening, interactions having monomeric half-lives of 0.1 sec can be detected with low false positive rates." [pmid:22414956] synonym: "avexis" EXACT PSI-MI-short [] synonym: "AVidity-based EXtracellular Interaction Screen" EXACT PSI-MI-alternate [] synonym: "avidity-based extracellular interaction screen" EXACT PSI-MI-alternate [] is_a: MI:0892 ! solid phase assay created_by: ppm creation_date: 2015-06-01T15:05:13Z [Term] id: MI:2190 name: long non-coding ribonucleic acid def: "Non-protein coding transcripts longer than 200 nucleotides and that can be involved in a number of functions, like transcription, post-translational and epigenetic regulation. Most lncRNAs do not have a known function so far." [PMID:23750541] synonym: "lncrna" EXACT PSI-MI-short [] synonym: "lncRNA" EXACT PSI-MI-alternate [] synonym: "long non coding ribonucleic acid" EXACT PSI-MI-alternate [] synonym: "long non coding RNA" EXACT PSI-MI-alternate [] synonym: "long non-coding RNA" EXACT PSI-MI-alternate [] is_a: MI:0320 ! ribonucleic acid created_by: ppm creation_date: 2015-06-02T11:33:27Z [Term] id: MI:2191 name: clip def: "Combination of cross-linking and co-immunoprecipitation aimed to find protein-RNA interactions. The canonical method uses first a cross-linking procedure over a tissue sample or lysate, and the immunoprecipitated with specific antibodies for the protein of interest. Unspecific proteins are digested via proteinase K treatment. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA.\nhttps://en.wikipedia.org/wiki/CLIP" [PMID:14615540] subset: PSI-MI_slim synonym: "CLIP" EXACT PSI-MI-alternate [] synonym: "clip" EXACT PSI-MI-short [] synonym: "cross linking immunoprecipitation" EXACT PSI-MI-alternate [] synonym: "cross-linking immunoprecipitation" EXACT PSI-MI-alternate [] is_a: MI:0430 ! nucleic acid uv cross-linking assay created_by: ppm creation_date: 2015-06-15T10:17:34Z [Term] id: MI:2192 name: clip-seq def: "This method combines UV cross-linking and immunoprecipitation with high-throughput sequencing to identify binding sites of RNA-binding proteins.\nhttps://en.wikipedia.org/wiki/HITS-CLIP" [PMID:18978773, PMID:21633356] subset: PSI-MI_slim synonym: "CLIP-Seq" EXACT PSI-MI-alternate [] synonym: "clip-seq" EXACT PSI-MOD-short [] synonym: "HITS-CLIP" EXACT PSI-MI-alternate [] synonym: "UV cross-linking immunoprecipitation combined with high-throughput sequencing" EXACT PSI-MI-alternate [] is_a: MI:2191 ! clip created_by: ppm creation_date: 2015-06-15T10:44:44Z [Term] id: MI:2193 name: iclip def: "iCLIP allows for the stringent purification of UV cross-linked protein-RNA complexes, using immunoprecipitation followed by SDS-PAGE and membrane transfer. The radiolabelled protein-RNA complexes are then excised from the membrane, and treated with proteinase to release the RNA. This leaves one or two amino acids at the RNA cross-link site. The RNA is then reverse transcribed using barcoded primers. Because reverse transcription stops prematurely at the cross-link site, iCLIP allows RNA-protein interaction sites to be identified at high resolution.\nhttps://en.wikipedia.org/wiki/ICLIP" [PMID:20601959] subset: PSI-MI_slim synonym: "iclip" EXACT PSI-MI-short [] synonym: "iCLIP" EXACT PSI-MI-alternate [] synonym: "individual-nucleotide resolution cross-linking and immunoprecipitation" EXACT PSI-MI-alternate [] is_a: MI:2191 ! clip created_by: ppm creation_date: 2015-06-15T11:17:22Z [Term] id: MI:2194 name: crac def: "Combination of UV cross-linking and affinity purification where the protein of interest bears a tag used for pull-down or immunoprecipitation. As in CLIP, unspecific proteins are digested via proteinase K treatment and RNAs are tagged with oligonucleotide linkers. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA." [PMID:19482942] synonym: "crac" EXACT PSI-MI-short [] synonym: "CRAC" EXACT PSI-MI-alternate [] synonym: "cross-linking and analysis of cDNAs" EXACT PSI-MI-alternate [] is_a: MI:0430 ! nucleic acid uv cross-linking assay created_by: ppm creation_date: 2015-06-15T11:26:33Z [Term] id: MI:2195 name: clash def: "This method is a variation of CRAC where after combined cross-linking and affinity purification of protein-RNA complexes, RNA-RNA interactions are specifically detected. Base-paired RNA molecules can be linked together while tagging RNA with oligonucleotides, generating chimeric RNAs that allow identification of RNA-RNA pairs." [PMID:21610164] subset: PSI-MI_slim synonym: "clash" EXACT PSI-MI-short [] synonym: "CLASH" EXACT PSI-MI-alternate [] synonym: "cross-linking, ligation, and sequencing of hybrids" EXACT PSI-MI-alternate [] is_a: MI:2194 ! crac created_by: ppm creation_date: 2015-06-15T11:45:38Z [Term] id: MI:2196 name: quartz crystal microbalance def: "A method that monitors ligand binding by measuring the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator." [PMID:23504432] subset: PSI-MI_slim synonym: "qcm" EXACT PSI-MI-short [] synonym: "QCM" EXACT PSI-MI-alternate [] is_a: MI:0968 ! biosensor created_by: ppm creation_date: 2015-07-07T09:46:51Z [Term] id: MI:2197 name: probe interaction assay def: "An assay that uses molecular probes, such as ions, small molecules or antibodies to monitor interactions between biomolecules under study." [PMID:14755292] subset: PSI-MI_slim synonym: "probe interaction assay" EXACT PSI-MI-short [] is_a: MI:0401 ! biochemical created_by: ppm creation_date: 2015-07-07T10:11:26Z [Term] id: MI:2198 name: labelling assay def: "The interaction is inferred from the effect it exerts on specific chemical labelling of one of the interacting partners." [PMID:14755292] subset: PSI-MI_slim synonym: "labelling assay" EXACT PSI-MI-short [] is_a: MI:2197 ! probe interaction assay created_by: ppm creation_date: 2015-07-07T10:14:29Z [Term] id: MI:2199 name: specific site-labelling technology def: "The interaction is detected through selective, chemical blockage of a specific site -which can be an active site- that becomes inaccessible once the participants are interacting. The interaction is detected through loss of signal of the chemical label" [PMID:8441405] subset: PSI-MI_slim synonym: "site-labelling technology" EXACT PSI-MI-short [] synonym: "specific site-labelling technology" EXACT PSI-MI-alternate [] is_a: MI:2198 ! labelling assay created_by: ppm creation_date: 2015-07-07T11:51:57Z [Term] id: MI:2200 name: primesdb def: "PRIMESDB is a systems biology platform that is developed to enable the collection, integration and analysis of state-of-the-art genomics, proteomics and mathematical modelling data being generated by the PRIMES project. PRIMES iinvestigates the role of protein interaction machines in oncogenic signalling with a particular focus on the EGFR network. PRIMESDB provides a centralised knowledgebase and analysis platform for cancer protein interaction networks.\nhttp://primesdb.eu/" [PMID:22453911] synonym: "primesdb" EXACT PSI-MI-short [] synonym: "PRIMESDB" EXACT PSI-MI-alternate [] is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2015-07-13T16:36:21Z [Term] id: MI:2201 name: DNA chemical modification def: "Chemical alterations occurring at the nucleotide level in the specific DNA molecule involved in an interaction. The process can involve covalent modifications (i.e. methylations) or other forms of chemical modification." [PMID:14755292] subset: PSI-MI_slim synonym: "dna chemical modification" EXACT PSI-MI-short [] synonym: "DNA chemical modification" EXACT PSI-MI-alternate [] synonym: "DNA epigenetic modification" EXACT PSI-MI-alternate [] is_a: MI:0252 ! biological feature created_by: ppm creation_date: 2015-08-11T15:37:49Z [Term] id: MI:2202 name: RNA chemical modification def: "Chemical alterations occurring at the nucleotide level in the specific RNA molecule involved in an interaction. The process can involve covalent modifications (i.e. 2'-O-methylation) or other forms of chemical modification, such as isomerizations (i.e. pseudouridylation)." [PMID:14755292] subset: PSI-MI_slim synonym: "post-transcriptional modification" EXACT PSI-MI-alternate [] synonym: "rna chemical modification" EXACT PSI-MI-short [] synonym: "RNA chemical modification" EXACT PSI-MI-alternate [] is_a: MI:0252 ! biological feature created_by: ppm creation_date: 2015-08-11T15:55:40Z [Term] id: MI:2203 name: primer extension assay def: "Primer extension can be used to determine the 3' end of a given sequence of RNA. This technique requires a radiolabelled primer which is complementary to a region near the 3' end of the RNA. The primer is allowed to anneal to the RNA and reverse transcriptase is used to synthesize a strand of DNA from the RNA until it reaches the 5' end of the RNA. By denaturing the hybrid and using the extended primer DNA strand as a marker on an electrophoretic gel, it is possible to determine the transcriptional start site." [PMID:23378648] subset: PSI-MI_slim synonym: "primer extension assay" EXACT PSI-MI-short [] is_a: MI:1193 ! partial RNA sequence identification created_by: ppm creation_date: 2015-08-11T17:22:38Z [Term] id: MI:2204 name: micro rna def: "A micro RNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals, and some viruses, which functions in RNA silencing and post-transcriptional regulation of gene expression." [PMID:14744438, XX:] subset: PSI-MI_slim synonym: "micro RNA" EXACT PSI-MI-alternate [] synonym: "micro-RNA" EXACT PSI-MI-alternate [] synonym: "micro-rna" EXACT PSI-MI-alternate [] synonym: "mirna" EXACT PSI-MI-short [] synonym: "miRNA" EXACT PSI-MI-alternate [] xref: url: "https://en.wikipedia.org/wiki/MicroRNA" is_a: MI:0320 ! ribonucleic acid created_by: ppm creation_date: 2016-01-20T16:25:10Z [Term] id: MI:2205 name: pir def: "The PIR-International Protein Sequence Database (PIR-PSD) was the world's first database of classified and functionally annotated protein sequences that grew out of the Atlas of Protein Sequence and Structure (1965-1978) edited by Margaret Dayhoff. Produced and distributed by the Protein Information Resource in collaboration with MIPS (Munich Information Center for Protein Sequences) and JIPID (Japan International Protein Information Database), PIR-PSD has been the most comprehensive and expertly-curated protein sequence database in the public domain for over 20 years. In 2002, PIR joined EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics) to form the UniProt consortium. PIR-PSD sequences and annotations have been integrated into UniProt Knowledgebase. Bi-directional cross-references between UniProt (UniProt Knowledgebase and/or UniParc) and PIR-PSD are established to allow easy tracking of former PIR-PSD entries. PIR-PSD unique sequences, reference citations, and experimentally-verified data can now be found in the relevant UniProt records. \n\nLegacy data can be found at \nhttp://pir.georgetown.edu/pirwww/dbinfo/pir_psd.shtml" [] subset: PSI-MI_slim synonym: "pir" EXACT PSI-MI-short [] synonym: "PIR" EXACT PSI-MI-alternate [] synonym: "Protein Information Resource" EXACT PSI-MI-alternate [] is_a: MI:1096 ! protein sequence databases created_by: ppm creation_date: 2016-01-20T16:48:10Z [Term] id: MI:2206 name: observed nucleic acid chemical modification def: "Chemical modification observed on a nucleic acid molecule in the context of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition." [PMID:14755292] subset: PSI-MI_slim synonym: "observed na chemical modification" EXACT PSI-MI-alternate [] synonym: "observed nucleic acid chemical modification" EXACT PSI-MI-short [] is_a: MI:0668 ! feature attribute name created_by: ppm creation_date: 2016-01-21T14:50:29Z [Term] id: MI:2207 name: resulting nucleic acid chemical modification def: "Chemical modification observed on an RNA molecule resulting subsequently of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition." [PMID:14755292] subset: PSI-MI_slim synonym: "resulting na chemical modification" EXACT PSI-MI-alternate [] synonym: "resulting nucleic acid chemical modification" EXACT PSI-MI-short [] is_a: MI:2206 ! observed nucleic acid chemical modification created_by: ppm creation_date: 2016-01-21T15:02:23Z [Term] id: MI:2208 name: prerequisite-nucleic acid chemical modification def: "Chemical modification observed on a nucleic acid molecule required for an interaction to occur. Modifications involving full nucleotide substitutions/deletions are excluded from this definition." [PMID:14755292] subset: PSI-MI_slim synonym: "prerequisite-na chemical modification" EXACT PSI-MI-alternate [] synonym: "prerequisite-nucleic acid chemical modification" EXACT PSI-MI-short [] is_a: MI:2206 ! observed nucleic acid chemical modification created_by: ppm creation_date: 2016-01-21T15:12:35Z [Term] id: MI:2209 name: nucleic acid chemical modification decreasing an interaction def: "Chemical modification observed on a nucleic acid molecule observed to decrease the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition." [PMID:14755292] synonym: "na chemical modification decreasing" EXACT PSI-MI-short [] synonym: "nucleic acid chemical modification decreasing an interaction" EXACT PSI-MI-alternate [] is_a: MI:2206 ! observed nucleic acid chemical modification created_by: ppm creation_date: 2016-01-21T15:17:08Z [Term] id: MI:2210 name: nucleic acid chemical modification disrupting an interaction def: "Chemical modification observed on a nucleic acid molecule observed to disrupt an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition." [PMID:14755292] subset: PSI-MI_slim synonym: "na chemical modification disrupting" EXACT PSI-MI-short [] synonym: "nucleic acid chemical modification disrupting an interaction" EXACT PSI-MI-alternate [] is_a: MI:2206 ! observed nucleic acid chemical modification created_by: ppm creation_date: 2016-01-21T15:18:52Z [Term] id: MI:2211 name: nucleic acid chemical modification increasing an interaction def: "Chemical modification observed on a nucleic acid molecule observed to increase the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition." [PMID:14755292] subset: PSI-MI_slim synonym: "na chemical modification increasing" EXACT PSI-MI-short [] synonym: "nucleic acid chemical modification increasing an interaction" EXACT PSI-MI-alternate [] is_a: MI:2206 ! observed nucleic acid chemical modification created_by: ppm creation_date: 2016-01-21T15:25:51Z [Term] id: MI:2212 name: proteomexchange def: "The ProteomeXchange consortium was set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. The data is actually hosted by consortium member databases like PeptideAtlas or PRIDE. \n\nhttp://www.proteomexchange.org" [PMID:25047258] subset: PSI-MI_slim synonym: "proteomexchange" EXACT PSI-MI-short [] synonym: "ProteomExchange" EXACT PSI-MI-alternate [] is_a: MI:0737 ! peptide sequence database created_by: ppm creation_date: 2016-02-02T13:52:54Z [Term] id: MI:2213 name: super-resolution microscopy def: "Super-resolution microscopy is a form of light microscopy that allows images to be taken with a higher resolution than the diffraction limit. Several different methods can be used to achieve beyond-diffraction limit resolution and these can be broadly divided in two categories: \"true\" super-resolution techniques, which capture information contained in evanescent waves, and \"functional\" super-resolution techniques, which use clever experimental techniques and known limitations on the matter being imaged to reconstruct a super-resolution image." [PMID:14755292] synonym: "super resolution microscopy" EXACT PSI-MI-alternate [] synonym: "super-resolution microscopy" EXACT PSI-MI-short [] is_a: MI:0428 ! imaging technique created_by: ppm creation_date: 2016-02-11T11:10:32Z [Term] id: MI:2214 name: signor def: "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms." [PMID:26467481] subset: PSI-MI_slim synonym: "SIGnaling Network Open Resource" EXACT PSI-MI-alternate [] synonym: "signaling network open resource" EXACT PSI-MI-alternate [] synonym: "SIGNOR" EXACT PSI-MI-alternate [] synonym: "signor" EXACT PSI-MI-short [] xref: search-url: "http://signor.uniroma2.it/relation_result.php?id=${ac}/" is_a: MI:1106 ! pathways database created_by: ppm creation_date: 2016-03-15T15:31:08Z [Term] id: MI:2215 name: barcode fusion genetics two hybrid def: "This method allows screening of a full matrix of protein pairs in a single multiplexed strain pool. A doubly engineered clone pool is prepared so that each clone bears two distinct DNA barcodes flanked by site specific recombination sequences. Positive bait-prey combinations allow activation of reporter genes and their respective barcodes undergo recombination, creating unique barcode combinations. Recombined barcode tags are then fused, extracted and sequenced for identification of interacting pairs." [PMID:27107012] synonym: "barcode fusion genetics two hybrid" EXACT PSI-MI-alternate [] synonym: "bfg two hybrid" EXACT PSI-MI-alternate [] synonym: "bfg-2h" EXACT PSI-MI-short [] synonym: "BGF-2h" EXACT PSI-MI-alternate [] is_a: MI:1113 ! two hybrid bait and prey pooling approach created_by: ppm creation_date: 2016-05-05T14:33:32Z [Term] id: MI:2216 name: deampylation assay def: "Measurement of de-AMPylation, the removal of a phosphodiester or phosphoramide ester of AMP from Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino\nacids." [PMID:14755292] subset: PSI-MI_slim synonym: "de-ampylation assay" EXACT PSI-MI-alternate [] synonym: "de-AMPylation assay" EXACT PSI-MI-alternate [] synonym: "deampylation assay" EXACT PSI-MI-short [] synonym: "deAMPylation assay" EXACT PSI-MI-alternate [] is_a: MI:0415 ! enzymatic study created_by: ppm creation_date: 2016-05-09T09:40:07Z [Term] id: MI:2217 name: luciferase-c def: "The c-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." [PMID:22070901] subset: PSI-MI_slim synonym: "luciferase-c" EXACT PSI-MI-short [] is_a: MI:1205 ! luciferase tag created_by: ppm creation_date: 2016-05-09T09:45:05Z [Term] id: MI:2218 name: luciferase-n def: "The n-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." [PMID:22070901] subset: PSI-MI_slim synonym: "luciferase-n" EXACT PSI-MI-short [] is_a: MI:1205 ! luciferase tag created_by: ppm creation_date: 2016-05-09T09:45:23Z [Term] id: MI:2219 name: gaussia luciferase protein tag def: "Gaussia luciferase, is an enzyme from the crustacean Gaussia princeps catalyzing the oxidation of coelenterazine to coelenteramide that produces light. Gaussia luciferase produces a blue light around the 480 nm range." [PMID:26025768] synonym: "gaussia luciferase" EXACT PSI-MI-short [] synonym: "gaussia luciferase protein tag" EXACT PSI-MI-alternate [] synonym: "GLuc tag" EXACT PSI-MI-alternate [] synonym: "gluc tag" EXACT PSI-MOD-alternate [] is_a: MI:1205 ! luciferase tag created_by: ppm creation_date: 2016-05-09T10:05:39Z [Term] id: MI:2220 name: gaussia-c def: "The c-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." [PMID:17099704] synonym: "gaussia-c" EXACT PSI-MI-short [] is_a: MI:2219 ! gaussia luciferase protein tag created_by: ppm creation_date: 2016-05-09T10:13:06Z [Term] id: MI:2221 name: gaussia-n def: "The n-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." [PMID:17099704] synonym: "gaussia-n" EXACT PSI-MI-short [] is_a: MI:2219 ! gaussia luciferase protein tag created_by: ppm creation_date: 2016-05-09T10:13:23Z [Term] id: MI:2222 name: inference by socio-affinity scoring def: "Socio-affinity index provides a single measure of the association between each pair of proteins based on an entire AP-MS dataset, considering both the spoke (when one protein retrieves another when tagged) and the matrix (when two proteins are retrieved by another) evidence, and the overall frequency of each protein in the data set." [PMID:16429126] subset: PSI-MI_slim synonym: "inference by socio-affinity scoring" EXACT PSI-MI-alternate [] synonym: "socio-affinity index inference" EXACT PSI-MI-alternate [] synonym: "socio-affinity inference" EXACT PSI-MI-alternate [] synonym: "socioaffinity index scoring" EXACT PSI-MI-alternate [] synonym: "socioaffinity inference" EXACT PSI-MI-short [] is_a: MI:0363 ! inferred by author created_by: ppm creation_date: 2016-05-13T16:16:06Z [Term] id: MI:2223 name: inference by quantitative co-purification def: "This method measures co-purification of proteins through several orthogonal purification steps, deriving a set of correlation measures that are then computationally weighted and combined to infer interacting pairs." [PMID:27099342] subset: PSI-MI_slim synonym: "inference by quantitative co-purification" EXACT PSI-MI-short [] synonym: "quantitative tagless co - purification" EXACT PSI-MI-alternate [] is_a: MI:0363 ! inferred by author created_by: ppm creation_date: 2016-05-17T10:36:05Z [Term] id: MI:2224 name: chemical rna modification plus base pairing prediction def: "In this method predicted RNA-RNA pairings are tested by knocking down one of the two interacting RNAs and then experimentally determine if its presence is required for the other to be chemically modified." [PMID:10024243] subset: PSI-MI_slim synonym: "chemical rna modification plus base pairing prediction" EXACT PSI-MI-short [] is_a: MI:0254 ! genetic interference created_by: ppm creation_date: 2016-05-23T13:32:07Z [Term] id: MI:2225 name: zinc def: "ZINC is a database of commercially available compounds for virtual screening. It uses publicly available bioactivity data to allow investigators to access chemical tools for biology.\n\nhttp://zinc15.docking.org/" [PMID:26479676] subset: PSI-MI_slim synonym: "ZINC" EXACT PSI-MI-alternate [] synonym: "zinc" EXACT PSI-MI-short [] xref: id-validation-regexp: "[0-9]*" xref: search-url: "http://zinc15.docking.org/substances/${ac}" is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2016-06-13T15:47:30Z [Term] id: MI:2226 name: mutation with no effect def: "A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that does not have any effect over an interaction when compared with the wild-type." [PMID:14577292] subset: PSI-MI_slim synonym: "mutation not affecting interaction" EXACT PSI-MOD-alternate [] synonym: "mutation with no effect" EXACT PSI-MI-short [] is_a: MI:0118 ! mutation created_by: ppm creation_date: 2016-06-13T15:57:12Z [Term] id: MI:2227 name: mutation causing an interaction def: "A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that enables an interaction when compared with the wild-type, which does not interact." [PMID:14755292] synonym: "mutation causing" EXACT PSI-MI-short [] synonym: "mutation causing an interaction" EXACT PSI-MI-alternate [] synonym: "mutation enabling interaction" EXACT PSI-MI-alternate [] is_a: MI:0118 ! mutation created_by: ppm creation_date: 2016-06-13T16:25:47Z [Term] id: MI:2228 name: ceitec def: "Interactions and complexes curated by scientists at the Central European Institute of Technology (CEITEC)." [] synonym: "ceitec" EXACT PSI-MI-short [] synonym: "CEITEC" EXACT PSI-MI-alternate [] synonym: "Central European Institute of Technology" EXACT PSI-MI-alternate [] xref: search-url: "www.ceitec.eu/" is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2016-09-14T10:41:07Z [Term] id: MI:2229 name: nucleicacid-gene def: "Interaction between a nucleic acid and a gene region." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1046 ! interacting molecules created_by: ppm creation_date: 2016-09-21T11:39:49Z [Term] id: MI:2230 name: nucleicacid-nucleicacid def: "Interaction between a nucleic acid and a corresponding nucleic acid." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1046 ! interacting molecules created_by: ppm creation_date: 2016-09-21T11:41:03Z [Term] id: MI:2231 name: coexpression def: "This approach infers interacting pairs of proteins looking at expression data coming from transcript expression datasets. Co-expressed pairs of genes are ranked and predicted to be interacting proteins as well." [] subset: PSI-MI_slim synonym: "co-expression" EXACT PSI-MI-alternate [] synonym: "coexpression" EXACT PSI-MI-short [] synonym: "coexpression prediction" EXACT PSI-MI-alternate [] is_a: MI:0046 ! experimental knowledge based created_by: ppm creation_date: 2016-10-05T11:48:53Z [Term] id: MI:2232 name: molecular association def: "A particular way two or more molecules influence one another." [] subset: PSI-MI_slim synonym: "molecular association" EXACT PSI-MI-short [] is_a: MI:0190 ! interaction type created_by: ppm creation_date: 2016-12-08T15:17:45Z [Term] id: MI:2233 name: causal interaction def: "Binary causative relationships between biological entities. CV terms belonging to this term allow the description of causal interactions using the current PSI-MI schema." [DOI:10.1142/S0219525908001465] subset: PSI-MI_slim synonym: "causal interaction" EXACT PSI-MI-short [] relationship: part_of MI:0000 ! molecular interaction created_by: ppm creation_date: 2017-01-19T13:17:37Z [Term] id: MI:2234 name: causal statement def: "The effect of modulator entity A on a modulated entity B." [PMID:26467481] synonym: "causal statement" EXACT PSI-MI-short [] is_a: MI:2233 ! causal interaction created_by: ppm creation_date: 2017-01-19T13:20:22Z [Term] id: MI:2235 name: up-regulates def: "The effect of a modulator entity A on a modulated entity B that increases the concentration and/or frequency and/or rate and/or extent of the molecular function of B." [PMID:26467481] subset: PSI-MI_slim synonym: "activates" NARROW [] synonym: "up regulates" EXACT PSI-MI-alternate [] synonym: "up-regulates" EXACT PSI-MI-short [] is_a: MI:2234 ! causal statement created_by: ppm creation_date: 2017-01-19T13:47:54Z [Term] id: MI:2236 name: up-regulates activity def: "The effect of a modulator entity A on a modulated entity B that increases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093)." [PMID:26467481] subset: PSI-MI_slim synonym: "activates activity" EXACT PSI-MI-alternate [] synonym: "up-regulates activity" EXACT PSI-MI-short [] xref: GO:GO\:0044093 is_a: MI:2235 ! up-regulates created_by: ppm creation_date: 2017-01-19T13:50:43Z [Term] id: MI:2237 name: up-regulates quantity def: "The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B." [PMID:26467481] subset: PSI-MI_slim synonym: "increases quantity" EXACT PSI-MI-alternate [] synonym: "up-regulates quantity" EXACT PSI-MI-short [] is_a: MI:2235 ! up-regulates created_by: ppm creation_date: 2017-01-19T13:53:41Z [Term] id: MI:2238 name: up-regulates quantity by expression def: "The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B, by promoting its gene expression." [PMID:26467481] subset: PSI-MI_slim synonym: "increases quantity by expression" EXACT PSI-MI-alternate [] synonym: "up-regulates quantity by expression" EXACT PSI-MI-short [] is_a: MI:2237 ! up-regulates quantity created_by: ppm creation_date: 2017-01-19T13:56:00Z [Term] id: MI:2239 name: up-regulates quantity by stabilization def: "The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B by preventing its degradation." [PMID:26467481] subset: PSI-MI_slim synonym: "increases quantity by stabilization" EXACT PSI-MI-alternate [] synonym: "up-regulates quantity by stabilization" EXACT PSI-MI-short [] is_a: MI:2237 ! up-regulates quantity created_by: ppm creation_date: 2017-01-19T13:58:03Z [Term] id: MI:2240 name: down-regulates def: "The effect of a modulator entity A on a modulated entity B that decreases the concentration and/or frequency and/or ate and/or extent of molecular function of B." [PMID:26467481] subset: PSI-MI_slim synonym: "down regulates" EXACT PSI-MI-alternate [] synonym: "down-regulates" EXACT PSI-MI-short [] is_a: MI:2234 ! causal statement created_by: ppm creation_date: 2017-01-19T14:00:20Z [Term] id: MI:2241 name: down-regulates activity def: "The effect of a modulator entity A on a modulated entity B that decreases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093)." [PMID:26467481] subset: PSI-MI_slim synonym: "down-regulates activity" EXACT PSI-MI-short [] synonym: "inhibits activity" EXACT PSI-MI-alternate [] xref: GO:GO\:0044093 is_a: MI:2240 ! down-regulates created_by: ppm creation_date: 2017-01-19T14:13:34Z [Term] id: MI:2242 name: down-regulates quantity def: "The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B." [PMID:26467481] subset: PSI-MI_slim synonym: "decreases quantity" EXACT PSI-MI-alternate [] synonym: "down-regulates quantity" EXACT PSI-MI-short [] is_a: MI:2240 ! down-regulates created_by: ppm creation_date: 2017-01-19T14:15:10Z [Term] id: MI:2243 name: down-regulates quantity by repression def: "The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B, by preventing its gene expression." [PMID:26467481] subset: PSI-MI_slim synonym: "Decrease quantity by expression" EXACT PSI-MI-alternate [] synonym: "down-regulates quantity by repression" EXACT PSI-MI-short [] is_a: MI:2242 ! down-regulates quantity created_by: ppm creation_date: 2017-01-19T14:25:28Z [Term] id: MI:2244 name: down-regulates quantity by destabilization def: "The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B by promoting its degradation." [PMID:26467481] subset: PSI-MI_slim synonym: "decrease quantity by stabilization" EXACT PSI-MI-alternate [] synonym: "down-regulates quantity by destabilization" EXACT PSI-MI-short [] is_a: MI:2242 ! down-regulates quantity created_by: ppm creation_date: 2017-01-19T14:28:52Z [Term] id: MI:2245 name: causal regulatory mechanism def: "Type of relationship between entities involved in a causal interaction. This term is to be used only to describe the effect of a modulator entity A on a modulated entity B when A is not immediately upstream of B." [PMID:26467481] synonym: "causal regulatory mechanism" EXACT PSI-MI-short [] synonym: "indirect causal regulation" EXACT PSI-MI-alternate [] is_a: MI:2233 ! causal interaction created_by: ppm creation_date: 2017-01-19T15:44:29Z [Term] id: MI:2246 name: indirect causal regulation def: "The effect of a modulator entity A on a modulated entity B that occurs when A is not immediately upstream of B." [PMID:15845847] subset: PSI-MI_slim synonym: "indirect" EXACT PSI-MI-alternate [] synonym: "indirect causal regulation" EXACT PSI-MI-short [] is_obsolete: true created_by: ppm creation_date: 2017-01-19T15:45:44Z [Term] id: MI:2247 name: transcriptional regulation def: "Any process that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation." [PMID:25428369] subset: PSI-MI_slim synonym: "transcriptional regulation" EXACT PSI-MI-short [] is_a: MI:2245 ! causal regulatory mechanism created_by: ppm creation_date: 2017-01-19T15:47:39Z [Term] id: MI:2248 name: translation regulation def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA." [PMID:25428369] subset: PSI-MI_slim synonym: "translation regulation" EXACT PSI-MI-short [] synonym: "translational regulation" EXACT PSI-MI-alternate [] is_a: MI:2245 ! causal regulatory mechanism created_by: ppm creation_date: 2017-01-19T15:48:53Z [Term] id: MI:2249 name: post transcriptional regulation def: "Any process that control gene expression at the RNA level, between the transcription and the translation of the gene." [PMID:25428369] subset: PSI-MI_slim synonym: "post transcriptional regulation" EXACT PSI-MI-short [] synonym: "post-transcriptional regulation" EXACT PSI-MI-alternate [] is_a: MI:2245 ! causal regulatory mechanism created_by: ppm creation_date: 2017-01-19T15:54:32Z [Term] id: MI:2250 name: direct causal regulation def: "The effect of a modulator entity A on a modulated entity B that occurs when A is immediately upstream of B." [PMID:15845847] subset: PSI-MI_slim synonym: "direct" EXACT PSI-MI-alternate [] synonym: "direct causal regulation" EXACT PSI-MI-short [] is_obsolete: true created_by: ppm creation_date: 2017-01-19T15:56:00Z [Term] id: MI:2251 name: transcriptional regulation by direct binding of dbTF to DNA regulatory element def: "Direct binding of a DbTF to a DNA regulatory sequence that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation." [PMID:25428369] subset: PSI-MI_slim is_obsolete: true created_by: ppm creation_date: 2017-01-19T15:57:01Z [Term] id: MI:2252 name: guanine nucleotide exchange factor reaction def: "The process mediated by guanine nucleotide exchange factors (GEFs) that catalyze the exchange of bound GDP with cytosolic GTP." [PMID:23303910] subset: PSI-MI_slim synonym: "GEF reaction" EXACT PSI-MOD-short [] is_a: MI:0414 ! enzymatic reaction created_by: ppm creation_date: 2017-01-19T16:13:36Z [Term] id: MI:2253 name: gtpase-activating protein reaction def: "A family of cellular proteins able to increases the activity of a GTPase." [PMID:17173929] synonym: "GAP reaction" EXACT PSI-MI-short [] synonym: "GTPase-Accelerating Protein reaction" EXACT PSI-MI-alternate [] synonym: "RGS protein reaction" EXACT PSI-MI-alternate [] is_obsolete: true created_by: ppm creation_date: 2017-01-19T16:16:04Z [Term] id: MI:2254 name: chemical activation reaction def: "The effect of a chemical compound that results in the activation or in an increased activation of a target molecule." [PMID:26467481] subset: PSI-MI_slim synonym: "chemical activation reaction" EXACT PSI-MI-short [] is_obsolete: true created_by: ppm creation_date: 2017-01-19T16:23:55Z [Term] id: MI:2255 name: chemical inhibition reaction def: "The effect of a chemical compound that stops, prevents, or reduces the activity of a target molecule." [PMID:26467481] subset: PSI-MI_slim synonym: "chemical inhibition reaction" EXACT PSI-MI-short [] is_obsolete: true created_by: ppm creation_date: 2017-01-19T16:25:05Z [Term] id: MI:2256 name: relocalization def: "Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location." [PMID:26467481] subset: PSI-MI_slim synonym: "relocalization" EXACT PSI-MI-short [] is_obsolete: true created_by: ppm creation_date: 2017-01-19T16:26:15Z [Term] id: MI:2257 name: small molecule catalysis reaction def: "The chemical reactions and pathways resulting in the formation, breakdown, modification of small molecules." [PMID:26467481] subset: PSI-MI_slim synonym: "small molecule catalysis reaction" EXACT PSI-MI-short [] is_obsolete: true created_by: ppm creation_date: 2017-01-19T16:27:34Z [Term] id: MI:2258 name: xenobiotic def: "Molecule that encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity, which is not physiologically part of a cell, tissue, organ, or organism." [PMID:14755292] subset: PSI-MI_slim synonym: "chemical" EXACT PSI-MI-alternate [] synonym: "drug" EXACT PSI-MI-alternate [] synonym: "xenobiotic" EXACT PSI-MI-short [] is_a: MI:0328 ! small molecule created_by: ppm creation_date: 2017-01-19T16:46:33Z [Term] id: MI:2259 name: causal interactor type def: "Entity involved in a causative relationship. These terms have to be used as interactor types only if associated with causal statements." [PMID:26467481] synonym: "causal interactor type" EXACT PSI-MI-short [] is_a: MI:2233 ! causal interaction created_by: ppm creation_date: 2017-01-19T16:51:20Z [Term] id: MI:2260 name: stimulus def: "Any detectable change in the internal or external environment of a cell, tissue, organ, or organism." [PMID:14755292] subset: PSI-MI_slim synonym: "stimulus" EXACT PSI-MI-short [] is_a: MI:2259 ! causal interactor type created_by: ppm creation_date: 2017-01-19T16:52:44Z [Term] id: MI:2261 name: phenotype def: "Cellular phenotype is the conglomerate of multiple cellular processes involving gene and protein expression that result in the elaboration of a cell's particular morphology and function." [PMID:19380745] subset: PSI-MI_slim synonym: "phenotype" EXACT PSI-MI-short [] is_a: MI:2259 ! causal interactor type created_by: ppm creation_date: 2017-01-19T16:54:07Z [Term] id: MI:2262 name: causal regulatory modification def: "The modification of a subsequence that regulates the concentration and/or frequency and/or rate and/or extent of the molecular function of an entity." [PMID:26467481] comment: CAUTION: This is a temporary branch. These terms will be soon added in the PSI-MOD ontology and this branch will became obsolete. synonym: "causal regulatory modification" EXACT PSI-MI-short [] is_a: MI:2233 ! causal interaction created_by: ppm creation_date: 2017-01-19T17:03:04Z [Term] id: MI:2263 name: s-nitrosylation def: "Reaction that create a covalent bond between a nitrogen monoxide group and the thiol group of cysteine." [PMID:15688001] subset: PSI-MI_slim synonym: "s-nitrosylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: ppm creation_date: 2017-01-19T17:11:46Z [Term] id: MI:2264 name: tyrosinated residue def: "A protein modification that effectively add a tyrosine residues to the c-terminal end of alpha-tubulin." [PMID:26467481] subset: PSI-MI_slim synonym: "tyrosinated residue" EXACT PSI-MI-short [] is_a: MI:2262 ! causal regulatory modification created_by: ppm creation_date: 2017-01-23T10:26:40Z [Term] id: MI:2265 name: de-acetylated residue def: "A protein modification that effectively remove an acyl group from a protein." [PMID:26467481] subset: PSI-MI_slim synonym: "de-acetylated residue" EXACT PSI-MI-short [] synonym: "deacetylated residue" EXACT PSI-MI-alternate [] is_a: MI:2262 ! causal regulatory modification created_by: ppm creation_date: 2017-01-23T10:30:06Z [Term] id: MI:2266 name: de-phosphorylated residue def: "A protein modification that effectively remove a phosphate group from a protein by hydrolysis." [PMID:26467481] subset: PSI-MI_slim synonym: "de-phosphorylated residue" EXACT PSI-MI-short [] synonym: "dephosphorylated residue" EXACT PSI-MI-alternate [] is_a: MI:2262 ! causal regulatory modification created_by: ppm creation_date: 2017-01-23T10:32:50Z [Term] id: MI:2267 name: de-sumoylated residue def: "A protein modification that effectively cleaves the G-K bond and releases SUMO proteins." [PMID:26467481] subset: PSI-MI_slim synonym: "de-sumoylated residue" EXACT PSI-MI-short [] synonym: "desumoylated residue" EXACT PSI-MI-alternate [] is_a: MI:2262 ! causal regulatory modification created_by: ppm creation_date: 2017-01-23T10:46:01Z [Term] id: MI:2268 name: de-methylated residue def: "A protein modification that effectively removes one or more methyl groups from a protein." [PMID:26467481] subset: PSI-MI_slim synonym: "de-methylated residue" EXACT PSI-MI-short [] synonym: "demethylated residue" EXACT PSI-MI-alternate [] is_a: MI:2262 ! causal regulatory modification created_by: ppm creation_date: 2017-01-23T10:47:33Z [Term] id: MI:2269 name: de-ubiquitinylated residue def: "A protein modification that effectively cleaves the G-K bond and releases ubiquitin or ubiquitin like proteins." [PMID:26467481] subset: PSI-MI_slim synonym: "de-ubiquitinylated residue" EXACT PSI-MI-short [] synonym: "deubiquitinylated residue" EXACT PSI-MI-alternate [] is_a: MI:2262 ! causal regulatory modification created_by: ppm creation_date: 2017-01-23T10:48:53Z [Term] id: MI:2270 name: signalink def: "SignaLink 2.0 is a signaling pathway resource with multi-layered regulatory networks.\nhttp://signalink.org" [PMID:23331499] subset: PSI-MI_slim synonym: "SignaLink" EXACT PSI-MI-alternate [] synonym: "signalink" EXACT PSI-MI-short [] xref: url:http\://signalink.org is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2017-01-23T11:41:20Z [Term] id: MI:2271 name: edam def: "EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats.\nhttp://edamontology.org/" [PMID:23479348] subset: PSI-MI_slim synonym: "edam" EXACT PSI-MI-short [] synonym: "EDAM" EXACT PSI-MI-alternate [] synonym: "EMBRACE Data And Methods" EXACT PSI-MI-alternate [] xref: url:http\://edamontology.org/ is_a: MI:0461 ! interaction database created_by: ppm creation_date: 2017-01-26T15:09:47Z [Term] id: MI:2272 name: tyrosinylation def: "Reversible reaction that add a tyrosine residue to an amino-acid." [] subset: PSI-MI_slim synonym: "tyrosinylation" EXACT PSI-MI-short [] xref: GO:GO\:0018322 is_a: MI:0414 ! enzymatic reaction created_by: ppm creation_date: 2017-01-26T15:21:43Z [Term] id: MI:2273 name: tyrosination def: "Reversible reaction that add a tyrosine residues to the c-terminal end of alpha-tubulin." [PMID:10842328] subset: PSI-MI_slim synonym: "tyrosination" EXACT PSI-MI-short [] xref: GO:GO\:0018166 is_a: MI:2272 ! tyrosinylation created_by: ppm creation_date: 2017-01-26T15:22:39Z [Term] id: MI:2274 name: regulator def: "Entity whose activity exerts an effect on the concentration, frequency, rate or extent of the target entity." [PMID:14755292] subset: PSI-MI_slim synonym: "modulator" EXACT PSI-MI-alternate [] synonym: "regulator" EXACT PSI-MI-short [] is_a: MI:0500 ! biological role created_by: ppm creation_date: 2017-01-26T15:29:51Z [Term] id: MI:2275 name: regulator target def: "Entity whose concentration, frequency, rate or extent are regulated by the regulator entity." [PMID:14755292] subset: PSI-MI_slim synonym: "modulator target" EXACT PSI-MI-alternate [] synonym: "regulator target" EXACT PSI-MI-short [] is_a: MI:0500 ! biological role created_by: ppm creation_date: 2017-01-26T15:31:14Z [Term] id: MI:2276 name: carbohydrate chemical modification def: "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction. The process can involve covalent modifications (i.e. sulfations) or other forms of chemical modification." [PMID:14755292] synonym: "carbohydrate chemical modification" EXACT PSI-MI-short [] is_a: MI:0252 ! biological feature created_by: ppm creation_date: 2017-03-06T11:04:25Z [Term] id: MI:2277 name: Cr-two hybrid def: "This method uses Cre recombinase as a two-hybrid protein-protein interaction reporter that functions intracellularly to covalently and unidirectionally link interacting bait and prey plasmids via specialized loxP sites that flank the protein-coding sequences. The linked protein-coding sequences serve as interaction-identifying DNA molecules that enable massively multiplexed screening coupled with next-generation DNA sequencing to detect protein-protein interactions." [] subset: PSI-MI_slim synonym: "cr-2h" EXACT PSI-MI-alternate [] synonym: "cr-two hybrid" EXACT PSI-MI-short [] synonym: "Cre recombinase two hybrid" EXACT PSI-MI-alternate [] is_a: MI:1113 ! two hybrid bait and prey pooling approach created_by: ppm creation_date: 2017-06-20T15:57:41Z [Term] id: MI:2278 name: polymer chain length def: "Length of a repetitive polymer chain. Applicable to carbohydrates and other non-protein, non-nucleic acid polymers." [PMID:14755292] subset: PSI-MI_slim synonym: "polymer chain length" EXACT PSI-MI-short [] is_a: MI:0666 ! participant attribute name created_by: ppm creation_date: 2017-07-05T10:27:19Z [Term] id: MI:2279 name: complex portal def: "The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms, entered into the IntAct molecular interaction database . Data includes protein-only complexes as well as protein-small molecule and protein-nucleic acid complexes. All complexes are derived from physical molecular interaction evidences extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background. All complexes are tagged with Evidence and Conclusion Ontology codes to indicate the type of evidence available for each entry." [PMID:25313161] subset: PSI-MI_slim synonym: "Complex Portal" EXACT PSI-MI-alternate [] synonym: "complex portal" EXACT PSI-MI-short [] xref: search-url: "http://www.ebi.ac.uk/complexportal/complex/${ac}" is_a: MI:0461 ! interaction database is_a: MI:0473 ! participant database created_by: ppm creation_date: 2017-07-28T09:34:45Z [Term] id: MI:2280 name: deamidation reaction def: "Reaction in which an amide functional group in the side chain of the amino acids asparagine or glutamine is removed or converted to another functional group. Typically, asparagine is converted to aspartic acid or isoaspartic acid and glutamine is converted to glutamic acid or pyroglutamic acid (5-oxoproline)." [PMID:2703484, PMID:3440704] subset: PSI-MI_slim synonym: "deamidation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: ppm creation_date: 2017-08-08T14:38:29Z [Term] id: MI:2281 name: deamidation assay def: "Assay to measure the catalysis of the reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH3." [GO:0004040] subset: PSI-MI_slim synonym: "amidase assay" EXACT PSI-MI-alternate [] synonym: "deamidation" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: ppm creation_date: 2017-08-08T14:49:09Z [Term] id: MI:2282 name: complex-primary def: "Complex object unique primary identifier that is assigned to a complex in the Complex Portal." [PMID:25313161] subset: PSI-MI_slim synonym: "complex-primary" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type created_by: ppm creation_date: 2017-08-25T13:31:03Z [Term] id: MI:2283 name: southwestern blotting def: "Southwestern blotting, is a lab technique which involves identifying and characterizing DNA-binding proteins by their ability to bind to specific oligonucleotide probes, generally radioactively labeled. The proteins are separated by gel electrophoresis and are subsequently transferred to nitrocellulose membranes similar to other types of blotting." [PMID:26404144] subset: PSI-MI_slim synonym: "southwestern blot" EXACT PSI-MI-short [] synonym: "southwestern blotting" EXACT PSI-MI-alternate [] is_a: MI:0047 ! far western blotting created_by: ppm creation_date: 2017-11-15T15:35:20Z [Term] id: MI:2284 name: complex component def: "Indicates that the cross-referenced molecule is a component of a containing complex." [PMID:25313161] subset: PSI-MI_slim synonym: "complex component" EXACT PSI-MI-short [] synonym: "complex-component" EXACT PSI-MI-alternate [] is_a: MI:0353 ! cross-reference type created_by: ppm creation_date: 2017-12-15T11:08:53Z [Term] id: MI:2285 name: miRNA interference luciferase reporter assay def: "The method is based on the functional effect of the binding of the microRNA on the target (mRNA or LncRNA), which is the repression of the expression of the target. To validate a sequence as a direct target of a microRNA, a luciferase reporter gene carrying the wt candidate sequence or its mutated form is used, and the expression of the target is evaluated with a luciferase assay. If the wt is significantly less expressed than the mutant, the binding occurs." [PMID:14697198, PMID:21431711] subset: PSI-MI_slim synonym: "miRNA interference luciferase assay" EXACT PSI-MI-short [] is_a: MI:0255 ! post transcriptional interference created_by: pporras creation_date: 2018-05-02T15:22:12Z [Term] id: MI:2286 name: functional association def: "Binary relationship between biological entities when one of them modulates the other in terms of function, expression, degradation or stability of the other and the relationship between the partners cannot be ascertained as direct, so intermediate steps are implicitly present. This relation specifically does not imply a physical interaction between the entities involved." [] subset: PSI-MI_slim synonym: "functional association" EXACT PSI-MI-short [] is_a: MI:0190 ! interaction type created_by: pporras creation_date: 2018-06-27T15:24:40Z [Term] id: MI:2287 name: identification by structure determination def: "Identity of the participant was established (or confirmed) by\nfitting its molecular model to the experimentally determined\nelectron density." [PMID:7877166] subset: PSI-MI_slim synonym: "identification by structure determination" EXACT PSI-MI-alternate [] synonym: "structure determination" EXACT PSI-MI-short [] is_a: MI:0661 ! experimental participant identification created_by: pporras creation_date: 2018-06-28T15:00:41Z [Term] id: MI:2288 name: DAP-seq def: "DAP-seq is an in vitro TF-DNA binding assay in which a DAP-seq gDNA library is prepared by attaching a short DNA sequencing adaptor onto purified and fragmented gDNA. In a separate reaction, an affinity-purified TF is prepared by in vitro expression, bound to ligand-coupled beads, and washed to remove non-specific cellular components. The gDNA library is added to the affinity-bound TF and the unbound DNA is washed away. The bound fraction is eluted, amplified with PCR primers to introduce an indexed adaptor, and the DNA is sequenced." [PMID:27203113] subset: PSI-MI_slim synonym: "dap-seq" EXACT PSI-MI-short [] synonym: "DNA affinity purification sequencing" EXACT PSI-MI-alternate [] is_a: MI:0004 ! affinity chromatography technology created_by: pporras creation_date: 2018-06-28T16:09:45Z [Term] id: MI:2289 name: virotrap def: "The bait fused to a viral protein (e.g. HIV-1 GAG protein) allows the trapping of interaction partners (preys) within virus-like particles (VLPs) that bud from mammalian cells. Once the VLPs are enriched and purified, this technique allows the isolation of multimeric complexes as well as binary interactions and their subsequent identification by methods such as MS and western blots." [PMID:27122307] subset: PSI-MI_slim synonym: "viral particle co-purification" EXACT PSI-MI-alternate [] is_a: MI:0401 ! biochemical created_by: pporras creation_date: 2018-09-13T10:18:19Z [Term] id: MI:2290 name: optical tweezers def: "Optical tweezers are instruments that use a focused laser beam to apply force to particles suspended in a liquid medium. This allows to measure forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies." [PMID:17023539, PMID:17081984] subset: PSI-MI_slim is_a: MI:0859 ! force spectroscopy created_by: pporras creation_date: 2018-09-13T10:39:59Z [Term] id: MI:2291 name: atomic force microscopy cantilevers def: "Molecules adsorbed on a solid surface are picked up by a microscopic tip (nanometers wide) that is located at the end of an elastic cantilever. Piezoelectric controller is used to measure forces generated by single molecules or molecular complexes stretched between the substrate and the cantilever tip." [PMID:18511917] subset: PSI-MI_slim synonym: "afm cantilevers" EXACT PSI-MI-short [] is_a: MI:0859 ! force spectroscopy created_by: pporras creation_date: 2018-09-13T10:49:44Z [Term] id: MI:2292 name: magnetic tweezers def: "Magnetic tweezers are instruments that use a set of magnets to apply forces to physically hold and move individual molecules attached to ferromagnetic beads. Such instruments allow to measure the forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies." [PMID:18511917] subset: PSI-MI_slim synonym: "electromagnetic tweezers" EXACT PSI-MI-alternate [] is_a: MI:0859 ! force spectroscopy created_by: pporras creation_date: 2018-09-13T12:04:16Z [Term] id: MI:2293 name: 5' position def: "Term describing the upstream end of a nucleotide sequence." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0333 ! feature range status created_by: pporras creation_date: 2018-09-14T09:15:05Z [Term] id: MI:2294 name: 5' range def: "Term describing the upstream region of a nucleotide sequence, exact coordinates not available." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0333 ! feature range status created_by: pporras creation_date: 2018-09-14T09:25:33Z [Term] id: MI:2295 name: 3' position def: "Term describing the downstream end of a nucleotide sequence." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0333 ! feature range status created_by: pporras creation_date: 2018-09-14T09:26:47Z [Term] id: MI:2296 name: 3' range def: "Term describing the downstream region of a nucleotide sequence, exact coordinates not available." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0333 ! feature range status created_by: pporras creation_date: 2018-09-14T09:27:33Z [Term] id: MI:2297 name: carbohydrate chemical modification causing an interaction def: "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that enables an interaction when compared with the unaltered carbohydrate, which does not interact." [PMID:14755292] subset: PSI-MI_slim synonym: "carbohydrate chemical modification causing" EXACT PSI-MI-short [] is_a: MI:2276 ! carbohydrate chemical modification created_by: pporras creation_date: 2018-09-14T09:45:20Z [Term] id: MI:2298 name: carbohydrate chemical modification with no effect def: "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that does not have any effect over an interaction when compared with the unaltered form." [PMID:14755292] subset: PSI-MI_slim synonym: "carbohydrate chemical modification not affecting interaction" EXACT PSI-MI-alternate [] is_a: MI:2276 ! carbohydrate chemical modification created_by: pporras creation_date: 2018-09-14T09:49:02Z [Term] id: MI:2299 name: carbohydrate chemical modification decreasing interaction def: "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate." [PMID:14755292] subset: PSI-MI_slim synonym: "carbohydrate chemical modification decreasing" EXACT PSI-MI-short [] is_a: MI:2276 ! carbohydrate chemical modification created_by: pporras creation_date: 2018-09-14T09:53:05Z [Term] id: MI:2300 name: carbohydrate chemical modification decreasing interaction rate def: "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate." [PMID:14755292] subset: PSI-MI_slim synonym: "carbohydrate chemical modification decreasing rate" EXACT PSI-MI-short [] is_a: MI:2299 ! carbohydrate chemical modification decreasing interaction created_by: pporras creation_date: 2018-09-14T09:56:38Z [Term] id: MI:2301 name: carbohydrate chemical modification decreasing interaction strength def: "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength when compared with the unaltered carbohydrate." [PMID:14755292] subset: PSI-MI_slim synonym: "carbohydrate chemical modification decreasing strength" EXACT PSI-MI-short [] is_a: MI:2299 ! carbohydrate chemical modification decreasing interaction created_by: pporras creation_date: 2018-09-14T09:58:21Z [Term] id: MI:2302 name: carbohydrate chemical modification disrupting interaction def: "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate." [PMID:14755292] subset: PSI-MI_slim synonym: "carbohydrate chemical modification disrupting" EXACT PSI-MI-short [] is_a: MI:2299 ! carbohydrate chemical modification decreasing interaction created_by: pporras creation_date: 2018-09-14T10:03:25Z [Term] id: MI:2303 name: carbohydrate chemical modification disrupting interaction strength def: "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength when compared with the unaltered carbohydrate." [PMID:14755292] subset: PSI-MI_slim synonym: "carbohydrate chemical modification disrupting strength" EXACT PSI-MI-short [] is_a: MI:2302 ! carbohydrate chemical modification disrupting interaction created_by: pporras creation_date: 2018-09-14T10:06:44Z [Term] id: MI:2304 name: carbohydrate chemical modification disrupting interaction rate def: "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate." [PMID:14755292] subset: PSI-MI_slim synonym: "carbohydrate chemical modification disrupting rate" EXACT PSI-MI-short [] is_a: MI:2302 ! carbohydrate chemical modification disrupting interaction created_by: pporras creation_date: 2018-09-14T10:08:37Z [Term] id: MI:2305 name: carbohydrate chemical modification increasing interaction def: "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate." [PMID:14755292] subset: PSI-MI_slim synonym: "carbohydrate chemical modification increasing" EXACT PSI-MI-short [] is_a: MI:2276 ! carbohydrate chemical modification created_by: pporras creation_date: 2018-09-14T10:11:37Z [Term] id: MI:2306 name: carbohydrate chemical modification increasing interaction strength def: "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength when compared with the unaltered carbohydrate." [PMID:14755292] subset: PSI-MI_slim synonym: "carbohydrate chemical modification increasing strength" EXACT PSI-MI-short [] is_a: MI:2305 ! carbohydrate chemical modification increasing interaction created_by: pporras creation_date: 2018-09-14T10:22:03Z [Term] id: MI:2307 name: carbohydrate chemical modification increasing interaction rate def: "Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate." [PMID:14755292] subset: PSI-MI_slim synonym: "carbohydrate chemical modification increasing rate" EXACT PSI-MI-short [] is_a: MI:2305 ! carbohydrate chemical modification increasing interaction created_by: pporras creation_date: 2018-09-14T10:23:21Z [Term] id: MI:2308 name: attached carbohydrate def: "Carbohydrate species chemically attached to proteins, or other organic molecules." [PMID:14755292] comment: Specific carbohydrate species can be represented through the MOD ontology and their representation escapes the scope of this CV. subset: PSI-MI_slim synonym: "attached glycan" EXACT PSI-MI-alternate [] synonym: "glycosylation" EXACT PSI-MI-alternate [] is_a: MI:0252 ! biological feature created_by: pporras creation_date: 2018-09-14T10:26:12Z [Term] id: MI:2309 name: attached carbohydrate causing an interaction def: "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that enables an interaction when compared with the non-glycosylated molecule, which does not interact." [PMID:14755292] subset: PSI-MI_slim synonym: "attached carbohydrate causing" EXACT PSI-MI-short [] synonym: "glycosylation causing interaction" EXACT PSI-MI-alternate [] is_a: MI:2308 ! attached carbohydrate created_by: pporras creation_date: 2018-09-14T10:37:41Z [Term] id: MI:2310 name: attached carbohydrate with no effect def: "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that has no effect over an interaction when compared with the non-glycosylated molecule, which does not interact." [PMID:14755292] subset: PSI-MI_slim synonym: "attached carbohydrate not affecting interaction" EXACT PSI-MI-alternate [] synonym: "glycosylation with no effect" EXACT PSI-MI-alternate [] is_a: MI:2308 ! attached carbohydrate created_by: pporras creation_date: 2018-09-14T10:40:12Z [Term] id: MI:2311 name: attached carbohydrate decreasing interaction def: "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "attached carbohydrate decreasing" EXACT PSI-MI-short [] synonym: "glycosylation decreasing interaction" EXACT PSI-MI-alternate [] is_a: MI:2308 ! attached carbohydrate created_by: pporras creation_date: 2018-09-14T10:42:27Z [Term] id: MI:2312 name: attached carbohydrate increasing interaction def: "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "attached carbohydrate increasing" EXACT PSI-MI-short [] synonym: "glycosylation increasing interaction" EXACT PSI-MI-alternate [] is_a: MI:2308 ! attached carbohydrate created_by: pporras creation_date: 2018-09-14T10:46:39Z [Term] id: MI:2313 name: attached carbohydrate increasing interaction strength def: "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength when compared with the non-glycosylated molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "attached carbohydrate increasing strength" EXACT PSI-MI-short [] synonym: "glycosylation increasing strength" EXACT PSI-MI-alternate [] is_a: MI:2312 ! attached carbohydrate increasing interaction created_by: pporras creation_date: 2018-09-14T10:47:14Z [Term] id: MI:2314 name: attached carbohydrate increasing interaction rate def: "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "attached carbohydrate increasing rate" EXACT PSI-MI-short [] synonym: "glycosylation increasing rate" EXACT PSI-MI-alternate [] is_a: MI:2312 ! attached carbohydrate increasing interaction created_by: pporras creation_date: 2018-09-14T10:49:39Z [Term] id: MI:2315 name: attached carbohydrate disrupting interaction rate def: "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "attached carbohydrate disrupting rate" EXACT PSI-MI-short [] synonym: "glycosylation disrupting rate" EXACT PSI-MI-alternate [] is_a: MI:2311 ! attached carbohydrate decreasing interaction is_a: MI:2317 ! attached carbohydrate disrupting interaction created_by: pporras creation_date: 2018-09-14T10:50:23Z [Term] id: MI:2316 name: attached carbohydrate disrupting interaction strength def: "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength when compared with the non-glycosylated molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "attached carbohydrate disrupting strength" EXACT PSI-MI-short [] synonym: "glycosylation disrupting strength" EXACT PSI-MI-alternate [] is_a: MI:2311 ! attached carbohydrate decreasing interaction is_a: MI:2317 ! attached carbohydrate disrupting interaction created_by: pporras creation_date: 2018-09-14T10:51:06Z [Term] id: MI:2317 name: attached carbohydrate disrupting interaction def: "Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "attached carbohydrate disrupting" EXACT PSI-MI-short [] synonym: "glycosylation disrupting interaction" EXACT PSI-MI-alternate [] is_a: MI:2311 ! attached carbohydrate decreasing interaction created_by: pporras creation_date: 2018-09-18T09:11:58Z [Term] id: MI:2318 name: force measurement def: "A technique that measures forces generated by interactions between molecules." [PMID:14755292] subset: PSI-MI_slim synonym: "intermolecular force" EXACT PSI-MI-alternate [] synonym: "molecular force measurement" RELATED [] is_a: MI:0013 ! biophysical created_by: pporras creation_date: 2018-10-11T13:41:11Z [Term] id: MI:2319 name: surface force measurement def: "A technique that measures interaction force between two surfaces as they are brought together and retracted." [doi:10.1038/262774a0] subset: PSI-MI_slim synonym: "surface adhesion force measurement" RELATED [] is_a: MI:2318 ! force measurement created_by: pporras creation_date: 2018-10-11T13:44:53Z [Term] id: MI:2320 name: aruk-ucl def: "The Alzheimer's Research UK Gene Ontology Project represents a collaboration between University College London, the European Bioinformatics Institute (EBI) and the University of Manchester, funded by Alzheimer's Research UK. This annotation group is a member of the IMEx Consortium.\n\nwww.ucl.ac.uk/functional-gene-annotation/neurological" [] subset: PSI-MI_slim synonym: "Alzheimer's Research UK Gene Ontology Project" EXACT PSI-MI-alternate [] is_a: MI:0461 ! interaction database created_by: pporras creation_date: 2018-10-16T09:26:24Z [Term] id: MI:2321 name: high-throughput sequencing def: "High-throughput (a.k.a. \"next-generation\") sequencing applies to methods that allow for sequencing of genome-scale number of bases." [PMID:19900591] subset: PSI-MI_slim synonym: "next-generation sequencing" EXACT PSI-MI-alternate [] synonym: "ngs sequencing" EXACT PSI-MI-short [] is_a: MI:0078 ! nucleotide sequence identification created_by: pporras creation_date: 2018-11-13T14:59:35Z [Term] id: MI:2322 name: Illumina dye sequencing def: "This method generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence." [PMID:18987734] subset: PSI-MI_slim synonym: "illumina sequencing" EXACT PSI-MI-short [] synonym: "solexa sequencing" EXACT PSI-MI-alternate [] is_a: MI:2321 ! high-throughput sequencing created_by: pporras creation_date: 2018-11-13T15:23:38Z [Term] id: MI:2323 name: kiss def: "KISS (KInase Substrate Sensor) is a protein complementation technology that allows in situ analysis of protein-protein interactions in intact mammalian cells. In this method, which is derived from MAPPIT (mammalian protein-protein interaction trap), the bait protein is coupled to the kinase domain of TYK2, while the prey protein is fused to a fragment of the gp130 cytokine receptor chain. Bait and prey interaction leads to phosphorylation of the gp130 anchor by TYK2, followed by recruitment and activation of STAT3, resulting in transcription of a STAT3-dependent reporter system. This approach enables the identification of interactions between proteins, including transmembrane and cytosolic proteins, and their modulation in response to physiological or pharmacological challenges." [PMID:25154561, PMID:29855964] subset: PSI-MI_slim synonym: "kinase substrate sensor" EXACT PSI-MI-alternate [] synonym: "KISS" EXACT PSI-MI-alternate [] synonym: "kiss" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay created_by: pporras creation_date: 2019-04-02T09:58:26Z [Term] id: MI:2324 name: dbsnp def: "dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations." [PMID:11125122] subset: PSI-MI_slim synonym: "dbSNP" EXACT PSI-MI-alternate [] synonym: "dbsnp" EXACT PSI-MI-short [] is_a: MI:0447 ! feature database created_by: pporras creation_date: 2019-04-02T10:52:06Z [Term] id: MI:2325 name: nanoluc luciferase protein tag def: "NanoLuc luciferase (Nluc) is a small (19 kDa), highly stable, ATP independent, bioluminescent protein derived from the luciferase complex of the deep-sea shrimp O. gracilirostris." [PMID:22894855] subset: PSI-MI_slim synonym: "NanoLuc" EXACT PSI-MI-alternate [] synonym: "nanoluc luciferase" EXACT PSI-MI-alternate [] synonym: "nluc" EXACT PSI-MI-short [] synonym: "NLuc" EXACT PSI-MI-alternate [] is_a: MI:1205 ! luciferase tag created_by: pporras creation_date: 2019-04-11T14:07:06Z [Term] id: MI:2326 name: nanoluc-n def: "The n-terminus of the nanoluc luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." [] subset: PSI-MI_slim synonym: "N-terminal fragment of nanoluc luciferase" EXACT PSI-MI-alternate [] synonym: "nluc-n" EXACT PSI-MI-short [] is_a: MI:2325 ! nanoluc luciferase protein tag created_by: pporras creation_date: 2019-04-11T14:14:54Z [Term] id: MI:2327 name: nanoluc-c def: "The c-terminus of the nanoluc luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay." [] subset: PSI-MI_slim synonym: "C-terminal fragment of nanoluc luciferase" EXACT PSI-MI-alternate [] synonym: "nluc-c" EXACT PSI-MI-short [] is_a: MI:2325 ! nanoluc luciferase protein tag created_by: pporras creation_date: 2019-04-11T14:16:59Z [Typedef] id: contains name: contains namespace: PSI-MOD def: "'Entity A' contains 'Entity B' implies that 'Entity B' is a part of the structure of 'Entity A'." [PubMed:18688235] comment: The inverse relationship to "part of". is_transitive: true [Typedef] id: derives_from name: derives from namespace: PSI-MOD def: "'Entity A' derives_from 'Entity B' implies that 'Entity A' is chemically derived from 'Entity B'." [PubMed:18688235] is_transitive: true [Typedef] id: has_functional_parent name: has functional parent namespace: PSI-MOD def: "'Entity A' has_functional_parent 'Entity B' implies that 'Entity B' has at least one chacteristic group from which 'Entity A' can be derived by functional modification." [PubMed:18688235] comment: This relationship indicates that the formula and mass of the child are not inherited from the mass of the parent. is_transitive: true [Typedef] id: part_of name: part of def: "'Entity A' part_of 'Entity B' implies that 'Entity A' is a part of the structure of 'Entity B'." [PubMed:18688235] is_transitive: true